Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,517,271	A→G	S18P (TCC→CCC)	yncD ←	TonB‑dependent receptor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,517,271	0	A	G	94.4%	113.1 / ‑0.9	36	S18P (TCC→CCC)	yncD	TonB‑dependent receptor
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base G (22/12);  total (23/13)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.89e-01

GGTGTTGCCAGGCGCATCTCCTCGCCATCCACCACGCTTACTGCTGCTGGGGTATCCAGTTCTGAAACCACCTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGAAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAATTTATGGAAAATGAAACGGCACA  >  NZ_CP009273/1517144‑1517399                                                                                                                                |                                                                                                                                 ggTGTTGCCAGGCGCATCTCCTCGCCATCCACAACGCTTACTGCTGCTGGGGTATCCAGTTCTGAAACCACCTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAg                                                                                                                         >  1:672347/1‑137 (MQ=255)        ccAGGCGCATCTCCTCGCCATCCACCACGCTTACTGCTGCTGGGGTATCCAGTTCTGAAACCACCTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCggg                                                                                                                >  1:78193/1‑139 (MQ=255)                                    gCTTACTGCTGCTGGGGTATCCAGTTCTGAAACCACCTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATc                                                                                    >  2:184914/1‑139 (MQ=255)                                               ctgGGGTATCCAGTTCTGAAACCACCTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGaaaa                                                                          >  2:117883/1‑138 (MQ=255)                                                  gggTATCCAGTTCTGAAACCACCTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGc                                                                      <  1:117883/139‑1 (MQ=255)                                                       tCCAGTTCTGAAACCACCTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGcc                                                                     >  1:136682/1‑135 (MQ=255)                                                       tCCAGTTCTGAAACCACCTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGcc                                                                     <  2:136682/135‑1 (MQ=255)                                                       tCCAGTTCTGAAACCACCTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGt                                                                 >  2:558686/1‑139 (MQ=255)                                                       tCCAGTTCTGAAACCACCTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGt                                                                 >  1:507018/1‑139 (MQ=255)                                                           gTTCTGAAACCACCTGCGGTG‑GGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGa                                                            <  1:699381/139‑1 (MQ=255)                                                            ttCTGAAACCACCTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAg                                                             >  1:746013/1‑138 (MQ=255)                                                                        cTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGc                                                >  2:408619/1‑139 (MQ=255)                                                                           cggtgcggCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGt                                             <  2:273586/139‑1 (MQ=255)                                                                                cggCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATgg                                        >  1:96824/1‑139 (MQ=255)                                                                                   cACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTaa                                     >  1:117902/1‑139 (MQ=255)                                                                                        aCAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGaaa                                >  2:52108/1‑139 (MQ=255)                                                                                        aCAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGaaa                                >  2:317039/1‑139 (MQ=255)                                                                                        aCAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGaaa                                >  2:286545/1‑139 (MQ=255)                                                                                        aCAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGaaa                                >  2:113457/1‑139 (MQ=255)                                                                                                  tCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGaa                                 <  1:285332/128‑1 (MQ=255)                                                                                                  tCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGaa                                 >  2:285332/1‑128 (MQ=255)                                                                                                  tCTGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTATGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAAtt                       >  2:653352/1‑138 (MQ=255)                                                                                                    tGTTCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAATTTAt                    >  1:358650/1‑139 (MQ=255)                                                                                                      ttCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAATTTATg                   >  1:522769/1‑138 (MQ=255)                                                                                                      ttCATCAGCGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAATTTATg                   >  1:20139/1‑138 (MQ=255)                                                                                                              cGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAATTTATGGAAAATGa           <  2:239805/138‑1 (MQ=255)                                                                                                              cGGCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAATTTATGGAAAATGa           >  1:239805/1‑138 (MQ=255)                                                                                                              cGGCAAAAACAACGGGGGAAAGGACAAGCAGTGCGGGCAAAACGGt                                                                                                       <  2:602344/46‑1 (MQ=255)                                                                                                              cGGCAAAAACAACGGGGGAAAGGACAAGCAGTGCGGGCAAAACGGt                                                                                                       >  1:602344/1‑46 (MQ=255)                                                                                                               ggCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAATTTATGGAAAATGaaa         <  1:113457/139‑1 (MQ=255)                                                                                                               ggCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAATTTATGGAAAATGaaa         <  2:358650/139‑1 (MQ=255)                                                                                                                gCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGc                                                                      >  2:750895/1‑77 (MQ=255)                                                                                                                gCAAAAACAACGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGc                                                                      <  1:750895/77‑1 (MQ=255)                                                                                                                     aacaacGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAATTTATGGAAAATGAAACGGcac   <  1:419561/139‑1 (MQ=255)                                                                                                                      acaacGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAATTTATGGAAAATGAAACGGcaca  <  2:20139/139‑1 (MQ=255)                                                                                                                      acaacGGGGGGAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAATTTATGGAAAATGAAACGGcaca  <  1:558686/139‑1 (MQ=255)                                                                                                                                |                                                                                                                                 GGTGTTGCCAGGCGCATCTCCTCGCCATCCACCACGCTTACTGCTGCTGGGGTATCCAGTTCTGAAACCACCTGCGGTGCGGCACTGACAATCATAGTCTGTTCATCAGCGGCAAAAACAACGGGGGAAAGGACAAGCAGTGCGGGCAAAACGGTCTGTCGGACGGAAAAAATCTTCATGAAAAAAGCCAGGTTAAGAATGGGAAAACGCCGTCATGGTAATGAAATTGTAAATTTATGGAAAATGAAACGGCACA  >  NZ_CP009273/1517144‑1517399

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑