Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	2,139,504	C→A	36.3%	L19L (CTG→CTT)	xtmA ←	terminase small subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,139,504	0	C	A	36.3%	9.7 / 5.6	11	L19L (CTG→CTT)	xtmA	terminase small subunit
Reads supporting (aligned to +/- strand):  ref base C (2/5);  new base A (2/2);  total (4/7)
Fisher's exact test for biased strand distribution p-value = 5.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.50e-01

ATCTTTTTGTTCTTGTATATATTGCTTGATGTGCGGCTTTTTCAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAACTCACTCATTTTATCACCCCCACAATTTTATCTAATATGGTTTCATACC  >  CP000730/2139390‑2139600                                                                                                                   |                                                                                                 atcttTTTGTTCTTGTNTATATTGCTTGANGTGTGGCTTCTTTAATAACCTACACCCTGTCACATGTGCACTATTTGCGCTATAACCTGCTTTTATGGCACTTTGTGTCACATTAAGTGTTCTTATATACTCATTCACaaa                                                                        >  1:114420/1‑141 (MQ=255) atcttTTTGTTCTTGTATATATTGCTTGATGTGTGGCTTCTTTAATAACCTACACCCTGTCACATGTGCACTATTTGCGCTATAACCTGCTTTTATGGCACTTTGTGTCACATTAAGTGTTCTTATATACTCATTCACaaa                                                                        >  1:9094/1‑141 (MQ=255)               gTATATATTGCTTGATGTGCGGCTTTTTCAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTg                                                          <  2:28553/141‑1 (MQ=255)                         cTTGATGTGCGGCTTTTTCAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAactc                                                <  1:5476/141‑1 (MQ=255)                         cTTGATGTGCGGCTTTTTCAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAactc                                                <  2:43617/141‑1 (MQ=255)                                           cAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAACTCACTCATTTTATCAccccc                              <  2:112308/141‑1 (MQ=255)                                               aaCCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAACTCACTCATTTTATCACCCCCACaa                          <  2:100901/141‑1 (MQ=255)                                                    acacGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAACTCACTCATTTTATCACCCCCACAATTTTa                     >  1:73958/1‑141 (MQ=255)                                                            tCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAACTCACTCATTTTATCACCCCCACAATTTTATCTAatat             >  2:43218/1‑141 (MQ=255)                                                                       cTATTTGCGCTATAACCTGCTTTTATGGCACTTTGTGTCACATTAAGTGTTCTTATATACTCATTCACAAAACGCGCTTGCTTTGCCGTTAACTCACTCATTCTATCACCTCCACAATTTTATCTAATAAGGTTTCATAcc  <  2:114420/141‑1 (MQ=255)                                                                       cTATTTGCGCTATAACCTGCTTTTATGGCACTTTGTGTCACATTAAGTGTTCTTATATACTCATTCACAAAACGCGCTTGCTTTGCCGTTAACTCACTCATTCTATCACCTCCACAATTTTATCTAATAAGGTTTCATAcc  <  2:9094/141‑1 (MQ=255)                                                                                                                   |                                                                                                 ATCTTTTTGTTCTTGTATATATTGCTTGATGTGCGGCTTTTTCAATAACCTACACGCTGTCACATGTGCGCTATTTGCGTTATATCCTGCTTTTATGGCACTTTGTGTTACATTCAGTGTTCTAATATACTCATTCACAAAACGTGCTTGCTTTGCAGTTAACTCACTCATTTTATCACCCCCACAATTTTATCTAATATGGTTTCATACC  >  CP000730/2139390‑2139600

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑