Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	5,539,546	C→T	8.4%	intergenic (‑412/+17)	CJ019_03622 ← / ← rlmB	IS110 family transposase ISPpu9/23S rRNA (guanosine‑2'‑O‑)‑methyltransferaseRlmB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	5,539,546	0	C	T	8.4%	148.8 / 2.8	47	intergenic (‑412/+17)	CJ019_03622/rlmB	IS110 family transposase ISPpu9/23S rRNA (guanosine‑2'‑O‑)‑methyltransferaseRlmB
Reads supporting (aligned to +/- strand):  ref base C (19/24);  new base T (2/2);  total (21/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCATCGGCAACTTGACCAGGAAGTCGC  >  KT2440/5539413‑5539675                                                                                                                                      |                                                                                                                                  gATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCg                                                                                                                                 <  7:278067/136‑1 (MQ=255)  aTCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCg                                                                                                                                 <  4:241467/135‑1 (MQ=255)  aTCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCg                                                                                                                                 <  7:240539/135‑1 (MQ=255)  aTCGCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGATGTGCGACCGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCg                                                                                                                                 <  4:184767/135‑1 (MQ=255)        aTGTCAGTCCAGATCTGACGTCATGCCCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCg                                                                                                                                 <  1:255722/129‑1 (MQ=255)                  aGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGt                                                                                                                  >  7:18905/1‑134 (MQ=255)                                 cgcATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAGGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGcc                                                                                                  >  5:228368/1‑135 (MQ=255)                                 cgcATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGcc                                                                                                  >  2:181975/1‑135 (MQ=255)                                       cTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGAc                                                                                            <  1:93105/135‑1 (MQ=255)                                         gTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGc                                                                                          >  3:272109/1‑135 (MQ=255)                                             gCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGc                                                                                     >  7:67400/1‑136 (MQ=255)                                                               ccGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAAccc                                                                    <  4:23409/135‑1 (MQ=255)                                                                      ggCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGc                                                             >  1:36605/1‑135 (MQ=255)                                                                      ggCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCCGTCGc                                                             >  3:98739/1‑135 (MQ=255)                                                                      ggCTGGGTGATCTCCTACAGGGGAACGCAATCACACTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGACCAGACACACCCCGGTCGcc                                                            >  7:21409/1‑136 (MQ=255)                                                                        cTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCAc                                                          <  7:210885/136‑1 (MQ=255)                                                                         tGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCTGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCAc                                                          <  2:11201/135‑1 (MQ=255)                                                                         tGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCAc                                                          <  3:144964/135‑1 (MQ=255)                                                                         tGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCAc                                                          <  3:37517/135‑1 (MQ=255)                                                                         tGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCAc                                                          <  1:25694/135‑1 (MQ=255)                                                                         ggggTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCAc                                                          <  1:36808/134‑1 (MQ=255)                                                                           ggTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGTCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCg                                                        >  1:129609/1‑135 (MQ=255)                                                                           ggTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGTCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCg                                                        >  1:125696/1‑135 (MQ=255)                                                                                  tcCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCGGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGt                                                  <  1:138090/134‑1 (MQ=255)                                                                                   ccTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCCCCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCGTGACCTGCCGCTGACGGCCGGCTTCGACCCGCCACACCCCGGTCGCCACCGCCCCGTTa                                                >  6:179894/1‑135 (MQ=37)                                                                                    cTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGt                                                  <  8:18905/132‑1 (MQ=255)                                                                                     tACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGTCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGt                                                  <  2:129609/131‑1 (MQ=255)                                                                                     tACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGTCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGt                                                  <  2:125696/131‑1 (MQ=255)                                                                                     tACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAg                                              >  4:39132/1‑135 (MQ=255)                                                                                             aaCGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGa                                      >  6:152649/1‑135 (MQ=255)                                                                                               cGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGc                                   >  7:262766/1‑136 (MQ=255)                                                                                               cGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGc                                   >  8:16312/1‑136 (MQ=255)                                                                                               cGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGc                                   >  8:257741/1‑136 (MQ=255)                                                                                                  aaTCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTa                                 >  4:169597/1‑135 (MQ=255)                                                                                                               gAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCATCGGc                     <  5:221229/134‑1 (MQ=255)                                                                                                               gAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCATCGGCa                    >  3:127109/1‑135 (MQ=255)                                                                                                                   gggTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCATCGGCAACtt                <  2:46699/135‑1 (MQ=255)                                                                                                                     gTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTc                                                                                  <  4:195356/67‑1 (MQ=255)                                                                                                                     gTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTc                                                                                  >  3:195356/1‑67 (MQ=255)                                                                                                                     gTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCATCGGCAACTTGAc             >  7:113119/1‑136 (MQ=255)                                                                                                                     gTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCGTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCCTCGGCAACTTGa              >  2:97102/1‑135 (MQ=255)                                                                                                                       tCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCATCGGCAACTTGAcc            <  2:264788/135‑1 (MQ=255)                                                                                                                               gAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCATCGGCAACTTGACCAGGAAGTc    <  5:204232/135‑1 (MQ=255)                                                                                                                               gAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCATCGGCAACTTGACCAGGAAGTc    <  4:34393/135‑1 (MQ=255)                                                                                                                               gAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCATCGGCAACTTGACCAGGAAGTc    <  2:66913/135‑1 (MQ=255)                                                                                                                               gAAGAGGCCGGAACAGGCTGAGAGGCAGCGCTGGCCCTGCCGCTGACGCACGGCTTCGAACAGCCAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCATCGGCAACTTGACCAGGAAGTc    <  6:34744/135‑1 (MQ=255)                                                                                                                                 agagGCCGGCACAGGCGGAGAGGCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCATCGGCAACTTGACCAGGAAGTCGc  <  1:251228/135‑1 (MQ=255)                                                                                                                                      |                                                                                                                                  GATCTCGATGTCAGTGCAGATCTGACGTCATGCGCATCCTGTTTGCTGTGCGACAGCGCAGCCCGGAAGGGCTGGGTGATCTCCTACAGGGGAACGCAATCACCCTGTAGGAGCGGGTTCACCCGCGAAGAGGCCGGAACAGGCTGAGAGTCAGCGCTTGACCTGCCGCTGACGCACGGCTTCGAACAGACAAACCCCGGTCGCCACCGACACGTTAAGGCTGCTGACGCTACCCGCCATCGGCAACTTGACCAGGAAGTCGC  >  KT2440/5539413‑5539675

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑