Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,657,601	G→A	intergenic (+34/+385)	hdeD → / ← arrS	acid‑resistance membrane protein/small regulatory RNA ArrS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,657,601	0	G	A	95.8%	74.1 / ‑4.0	24	intergenic (+34/+385)	hdeD/arrS	acid‑resistance membrane protein/small regulatory RNA ArrS
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (6/17);  total (6/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

AGCCTGTTCAGCTTCGCCAGTTTGTTCGTTAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTGATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAGATCAATTGCGCACTATCATTGAAATAAT  >  NC_000913/3657526‑3657677                                                                            |                                                                             aGCCTGTTCAGCTTCGCCAGTTTGTTCGTTAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTAAtgtg                                                                         <  1:652822/81‑1 (MQ=255)               cGCCAGTTTGTTCGTTAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGAt                                                            <  2:652823/80‑1 (MQ=255)                gCCAGTTTGTTCGTTAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGAtt                                                           <  1:652825/80‑1 (MQ=255)                gCCAGTTTGTTCGTTAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTa                                                          <  1:652824/81‑1 (MQ=255)                        gTTCGTTAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTAATActct                                                   <  2:652826/80‑1 (MQ=255)                          tCGTTAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTAATACtctctc                                                >  1:652848/1‑81 (MQ=255)                           cGTTAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTAATACtctctc                                                <  2:652827/80‑1 (MQ=255)                            gTTAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCg                                              <  2:652829/81‑1 (MQ=255)                            gTTAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCg                                              <  2:652828/81‑1 (MQ=255)                             ttAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGc                                             <  1:652830/81‑1 (MQ=255)                              tAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGc                                             >  2:652859/1‑80 (MQ=255)                                agcagcAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGCTa                                           <  2:652831/80‑1 (MQ=255)                                             aCCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAg                              <  1:652832/80‑1 (MQ=255)                                             aCCCCGGTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAg                              <  2:652833/80‑1 (MQ=255)                                              ccccGGTTGTCACCCGGATCATAGTCACTTGATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAGa                             <  2:652834/80‑1 (MQ=255)                                                   gTTGTCACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAGATCAAtt                       <  1:652835/81‑1 (MQ=255)                                                        cACCCGGATCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAGATCAATTGCGCa                  >  1:652853/1‑81 (MQ=255)                                                          cccGGATCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAGATCAATTGCGCACt                <  2:652836/81‑1 (MQ=255)                                                              gATCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAGATCAATTGCGCACTATCa            <  1:652837/81‑1 (MQ=255)                                                               aTCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAGATCAATTGCGCACTATCAt           >  1:652855/1‑81 (MQ=255)                                                               aTCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAGATCAATTGCGCACTATCAt           <  1:652838/81‑1 (MQ=255)                                                                tCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAGATCAATTGCGCACTATCAtt          >  1:652854/1‑81 (MQ=255)                                                                tCATAGTCACTTAATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAGATCAATTGCGCACTATCAtt          <  2:652839/81‑1 (MQ=255)                                                                        aCTTAATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAGATCAATTGCGCACTATCATTGAaataat  >  2:652860/1‑81 (MQ=255)                                                                            |                                                                             AGCCTGTTCAGCTTCGCCAGTTTGTTCGTTAAGCAGCAATAATTACCCCGGTTGTCACCCGGATCATAGTCACTTGATGTGACTATGATCCGATTAATACTCTCTCCGCTACGCAGTGTTGTAGATCAATTGCGCACTATCATTGAAATAAT  >  NC_000913/3657526‑3657677

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑