Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	200,214	C→T	P763S (CCA→TCA)	bamA →	BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	200,214	0	C	T	100.0%	169.0 / NA	52	P763S (CCA→TCA)	bamA	BamABCDE complex OM biogenesis outer membrane pore‑forming assembly factor
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (27/25);  total (27/25)

TTAGCGATAAGTATGCTAACTCGGTTCGTACTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATCCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCGTTGGTGTTCTCCTACGCCCAGCCGTTCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGTTTAACATCGGT  >  NC_000913/200101‑200348                                                                                                                  |                                                                                                                                       ttaGCGATAAGTATGCTAACTCGGTTCGTACTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCggg                                                                                                               <  1:1116286/139‑1 (MQ=255)       aTAAGTATGCTAACTCGGTTCGTACTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTAt                                                                                                            <  2:63051/136‑1 (MQ=255)       aTAAGTATGCTAACTCGGTTCGTACTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTAt                                                                                                            >  1:63051/1‑136 (MQ=255)         aaGTATGCTAACTCGGTTCGTACTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCAt                                                                                                       <  1:1173234/139‑1 (MQ=255)              tGCTAACTCGGTTCGTACTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACaa                                                                                                  >  1:981049/1‑139 (MQ=255)                   aCTCGGTTCGTACTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGAt                                                                                             >  2:643483/1‑139 (MQ=255)                      cGGTTCGTACTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTc                                                                                          <  2:650821/139‑1 (MQ=255)                      cGGTTCGTACTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTc                                                                                          >  1:650821/1‑139 (MQ=255)                         ttCGTACTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTa                                                                                                             <  2:1665571/117‑1 (MQ=255)                         ttCGTACTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTa                                                                                                             >  1:1665571/1‑117 (MQ=255)                              aCTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTgg                                                                                  <  1:643483/139‑1 (MQ=255)                                          tGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCa                                                                                                                                  >  2:1284019/1‑79 (MQ=255)                                          tGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCa                                                                                                                                  <  1:1284019/79‑1 (MQ=255)                                            ggATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCg                                                                                                          <  2:538480/101‑1 (MQ=255)                                            ggATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCg                                                                                                          >  1:538480/1‑101 (MQ=255)                                                 tGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCGTTGGTGTTCTCCTa                                                               >  2:1402299/1‑139 (MQ=255)                                                    gTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTg                                                                                                                   <  2:1681316/84‑1 (MQ=255)                                                    gTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTg                                                                                                                   >  1:1681316/1‑84 (MQ=255)                                                      aCCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCggg                                                                                                               >  1:1427622/1‑86 (MQ=255)                                                      aCCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCggg                                                                                                               <  2:1427622/86‑1 (MQ=255)                                                       ccGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGt                                                                                                                          <  2:1433112/74‑1 (MQ=255)                                                       ccGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGt                                                                                                                          >  1:1433112/1‑74 (MQ=255)                                                        cGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTAt                                                                                                            <  2:918099/87‑1 (MQ=255)                                                        cGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTAt                                                                                                            >  1:918099/1‑87 (MQ=255)                                                          tttGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCGTTg                                                                          <  1:1661011/119‑1 (MQ=255)                                                          tttGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCGTTg                                                                          >  2:1661011/1‑119 (MQ=255)                                                            tGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAat                                                                                                                                >  2:1266235/1‑63 (MQ=255)                                                            tGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAat                                                                                                                                <  1:1266235/63‑1 (MQ=255)                                                                  aCAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGGGGGTa                                                                                                             <  1:387150/76‑1 (MQ=255)                                                                  aCAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGGGGGTa                                                                                                             >  2:387150/1‑76 (MQ=255)                                                                  aCAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCGTTGGTGTTCTCCTACGCCCAGCCGTTCaaaa                                              >  2:754111/1‑139 (MQ=255)                                                                     aaCTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGAATGTCCCCATTGGGGCCGTTGGTGTTCTCCTACGCCCAGCGGTTCAAAACGt                                           <  2:981049/139‑1 (MQ=255)                                                                         gggATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAg                                                                                                                                    >  1:2501/1‑46 (MQ=255)                                                                         gggATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAg                                                                                                                                    <  2:2501/46‑1 (MQ=255)                                                                         gggATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCGTTGGTGTTCTCCTACGCCCAGCCGTTCAAAAAGTACGa                                       >  2:563440/1‑139 (MQ=255)                                                                           gATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACa                                                                                                   <  1:995021/77‑1 (MQ=255)                                                                           gATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACa                                                                                                   >  2:995021/1‑77 (MQ=255)                                                                                                 atCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCAt                                                                                                       >  2:1513598/1‑51 (MQ=255)                                                                                                 atCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCAt                                                                                                       <  1:1513598/51‑1 (MQ=255)                                                                                                  tCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGc                                                                               >  2:1647279/1‑74 (MQ=255)                                                                                                  tCCGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGc                                                                               <  1:1647279/74‑1 (MQ=255)                                                                                                   ccGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTa                                                                                                             <  2:1547069/43‑1 (MQ=255)                                                                                                   ccGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTa                                                                                                             >  1:1547069/1‑43 (MQ=255)                                                                                                   ccGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCGTTGGTGTTCTCCTACGCCCAGCCGTTCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGt             >  2:29603/1‑139 (MQ=255)                                                                                                   ccGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCGTTGGTGTTCTCCTACGCCCAGCCGTTCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGt             >  2:1511158/1‑139 (MQ=255)                                                                                                    cGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCg                                                                             <  2:2111/74‑1 (MQ=255)                                                                                                    cGGACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCg                                                                             >  1:2111/1‑74 (MQ=255)                                                                                                      gACTATAGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCGTTGGTGTTCTCCTACGCCCAGCCGTTCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGTTTa          >  2:885148/1‑139 (MQ=255)                                                                                                         tataGTGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCGTTGGTGTTCTCCTACGCCCAGCCGTTCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGTTTAACa       <  1:885148/139‑1 (MQ=255)                                                                                                            aGTGATTCAAGCAATATCCGTATGTCTGCGGGTAt                                                                                                            <  1:986773/35‑1 (MQ=255)                                                                                                            aGTGATTCAAGCAATATCCGTATGTCTGCGGGTAt                                                                                                            >  2:986773/1‑35 (MQ=255)                                                                                                              tGATTCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCGTTGGTGTTCTCCTACGCCCAGCCGTTCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGTTTAACATCGGt  <  1:1402299/139‑1 (MQ=255)                                                                                                                  |                                                                                                                                       TTAGCGATAAGTATGCTAACTCGGTTCGTACTTCCTTCTTCTGGGATATGGGTACCGTTTGGGATACAAACTGGGATTCCAGCCAATATTCTGGATATCCGGACTATAGTGATCCAAGCAATATCCGTATGTCTGCGGGTATCGCATTACAATGGATGTCCCCATTGGGGCCGTTGGTGTTCTCCTACGCCCAGCCGTTCAAAAAGTACGATGGAGACAAGGCAGAACAGTTCCAGTTTAACATCGGT  >  NC_000913/200101‑200348

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑