Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	KT2440	450,509	T→C	8.9%	T108A (ACC→GCC)	pqqE ←	PqqA peptide cyclase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	KT2440	450,509	0	T	C	8.9%	124.6 / 4.7	45	T108A (ACC→GCC)	pqqE	PqqA peptide cyclase
Reads supporting (aligned to +/- strand):  ref base T (23/18);  new base C (2/2);  total (25/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.86e-01

CCATTTCCAGCTTCTGTGCAAAAGCCTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTTCACCGCCGGAAAAGCCGATTTGTGCGGCACCCATTTCCCGC  >  KT2440/450377‑450642                                                                                                                                     |                                                                                                                                      ccATTTCCAGCTTCTGTGCAAAAGCCTTTTTCGAGCCGGCCTGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAg                                                                                                                                    <  7:55229/136‑1 (MQ=255)  cATTTCCAGCTTCTGTGCAAAAGCCTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGGCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAg                                                                                                                                    <  3:190372/135‑1 (MQ=255)          gCTTCTGTGCAAAAGCCTTTTTCGAGCCGGCCAGCTGGTTTTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGc                                                                                                                            <  4:181105/135‑1 (MQ=255)             tCTGTGCAAAAGCCTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGGCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGcc                                                                                                                           >  1:66033/1‑133 (MQ=255)             tCTGTGCAAAAGCCTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGc                                                                                                                            <  1:207618/132‑1 (MQ=255)             tCTGTGCAAAAGCCTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGc                                                                                                                            >  2:207618/1‑132 (MQ=255)             tCTGTGCAAAAGCCTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCACGCCGCCCTTCTTGAAGTCCGCGATGCGAGCCTCCGTCAGGCCAATGcc                                                                                                                           >  2:257175/1‑133 (MQ=255)                 tgCAAAAGCCTTTTTCGAGCCGGCCAGCAGGTTGTTCACCAGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGGCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGt                                                                                                                     >  7:181135/1‑135 (MQ=255)                  gCAATAGCCTTTTTCGAGCCGGCCAGCCGGTTGTGCACCTGCTCGTCGGTGGCCTGGAAGCTGATCTGGATTTGGTCCAGGCGGGCGTTCTTGAAGGCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGt                                                                                                                     <  6:169497/134‑1 (MQ=255)                  gCAAAAGCCTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCCGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGt                                                                                                                     <  5:222615/134‑1 (MQ=255)                  gCAAAAGCCTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGt                                                                                                                     <  3:258902/134‑1 (MQ=255)                  gCAAAAGCCTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGa                                                                                                                   >  8:188258/1‑136 (MQ=255)                        gCCTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAgg                                                                                                              <  4:120103/135‑1 (MQ=255)                         ccTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGCCAGGCCAATGCCCGAGGt                                                                                                                     >  2:270520/1‑127 (MQ=255)                         ccTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGCCAGGCCAATGCCCGAGGt                                                                                                                     >  2:267256/1‑127 (MQ=255)                         ccTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGCCAGGCCAATGCCCGAGGt                                                                                                                     <  1:270520/127‑1 (MQ=255)                         ccTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGCCAGGCCAATGCCCGAGGt                                                                                                                     <  1:267256/127‑1 (MQ=255)                                                ttgttCACCTGCTCGTCGCTGGCCTGGAAGCTGAGCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACggg                                                                                     <  7:157197/136‑1 (MQ=255)                                                 tgttCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACggg                                                                                     <  1:102435/135‑1 (MQ=255)                                                    tCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCctc                                                                                 >  8:44108/1‑136 (MQ=255)                                                    tCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCct                                                                                  >  2:238180/1‑135 (MQ=255)                                                            tcgtcgCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGAt                                                                           <  3:138329/134‑1 (MQ=255)                                                              gtcgCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCACGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAg                                                                        >  3:263878/1‑135 (MQ=255)                                                                cgCTGGCCTGGATGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGAGCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGCTCAgagg                                                                     >  8:133220/1‑133 (MQ=255)                                                                  cTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTgg                                                                    <  1:201302/135‑1 (MQ=255)                                                                  cTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTgg                                                                    <  2:47749/135‑1 (MQ=255)                                                                   tGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGCCGGGCCTCTGCGATCAGCTggg                                                                   >  8:136721/1‑135 (MQ=255)                                                                                 aTCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGGGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACg                                                      <  8:8266/134‑1 (MQ=255)                                                                                  tCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTa                                                    >  5:172029/1‑135 (MQ=255)                                                                                         atGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCgg                                             >  3:178950/1‑135 (MQ=255)                                                                                             tCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGGGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTTCa                                         <  3:133019/135‑1 (MQ=255)                                                                                              ccAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTTCAc                                        >  6:92574/1‑135 (MQ=255)                                                                                                   ccggccTTCTTGAAGTCGGCGATGGGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAgg                                                              <  7:151644/108‑1 (MQ=255)                                                                                                   ccggccTTCTTGAAGTCGGCGATGGGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAgg                                                              >  8:151644/1‑108 (MQ=255)                                                                                                   ccggccTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTTCAccgccg                                   >  7:181907/1‑135 (MQ=255)                                                                                                   ccggccTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTTCAccgccg                                   >  8:268822/1‑135 (MQ=255)                                                                                                   ccggccTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTACAccgcc                                    >  3:66271/1‑134 (MQ=255)                                                                                                   ccggccTTCTTGAAGTCGGCGATGCGCGCCTAGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCCGACGTACCAGCGGTTCAccgccg                                   >  4:195406/1‑135 (MQ=255)                                                                                                          tcttGAATTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTAGGTGTCGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGCCGTACCAGCGCTTCGCCGCCGGATAAGcc                           >  7:223281/1‑136 (MQ=255)                                                                                                          tcttGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTTCACCGCCGGAAAAGcc                           >  8:160773/1‑136 (MQ=255)                                                                                                          tcttGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTTCACCGCCGGAAAAGcc                           >  8:64966/1‑136 (MQ=255)                                                                                                          tcttGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTTCACCGCCGGAAAAGc                            >  6:258507/1‑135 (MQ=255)                                                                                                            ttGAAGGCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTTCACCGCCGGAAAAGcc                           <  5:208031/134‑1 (MQ=255)                                                                                                                       gATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTTCACCGCCGGAAAAGCCGATTTGTGCGGc               >  2:40469/1‑135 (MQ=255)                                                                                                                                    gTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTTCACCGCCGGAAAAGCCGATTTGTGCGGCACCCATTTCCcgc  <  2:66033/135‑1 (MQ=255)                                                                                                                                     |                                                                                                                                      CCATTTCCAGCTTCTGTGCAAAAGCCTTTTTCGAGCCGGCCAGCAGGTTGTTCACCTGCTCGTCGCTGGCCTGGAAGCTGATCTGGATATGGTCCAGGCCGGCCTTCTTGAAGTCGGCGATGCGCGCCTCGGTCAGGCCAATGCCCGAGGTGATCAGGTTGGTGTAGTAACCCAGGCGACGGGCCTCTGCGATCAGCTGGGCAAGGTCCTGACGTACCAGCGGTTCACCGCCGGAAAAGCCGATTTGTGCGGCACCCATTTCCCGC  >  KT2440/450377‑450642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑