Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	631,812	T→C	F640S (TTC→TCC)	cstA →	carbon starvation protein involved in peptide utilization, APC peptide transporter family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	631,812	0	T	C	96.9%	224.8 / ‑2.7	65	F640S (TTC→TCC)	cstA	carbon starvation protein involved in peptide utilization, APC peptide transporter family protein
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base C (31/32);  total (32/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.65e-01

GCAGGCTGGCAGAAAGCGTTTAGCCCGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTTCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCAACGGCGAAAGAAACGCCGTATGAAC  >  NC_000913/631679‑631946                                                                                                                                      |                                                                                                                                       gCAGGCTGGCAGAAAGCGTTTAGCCCGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCcaaca                                                                                                                                   <  2:965505/139‑1 (MQ=255) gCAGGCTGGCAGAAAGCGTTTAGCCCGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCcaaca                                                                                                                                   <  1:1326422/139‑1 (MQ=255)        ggCAGAAAGCGTTTAGCCCGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCt                                                                                                                            >  1:823048/1‑139 (MQ=255)        ggCAGAAAGCGTTTAGCCCGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCt                                                                                                                            >  1:398885/1‑139 (MQ=255)        ggCAGAAAGCGTTTAGCCCGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCt                                                                                                                            <  2:1432174/139‑1 (MQ=255)                         ccGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCcaac                                                                                                                                    >  2:1596882/1‑114 (MQ=255)                         ccGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCcaac                                                                                                                                    <  1:1596882/114‑1 (MQ=255)                          cGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCAt                                                                                                          <  2:1645071/139‑1 (MQ=255)                                                        cTAGTAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCaacaac                                                                                                                                 >  1:1151264/1‑86 (MQ=255)                                                        cTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCaacaac                                                                                                                                 <  2:1151264/86‑1 (MQ=255)                                                         taataaGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCt                                                                                                                            >  2:471995/1‑90 (MQ=255)                                                         taataaGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCt                                                                                                                            <  1:471995/90‑1 (MQ=255)                                                              aGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGtt                                                                      <  2:139381/139‑1 (MQ=255)                                                              aGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGtt                                                                      <  2:823048/139‑1 (MQ=255)                                                                ttCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTtct                                                                    >  2:1145568/1‑139 (MQ=255)                                                                  ccAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCTCAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGtggtgg                                                                                   >  2:1483768/1‑122 (MQ=255)                                                                  ccAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGtggtgg                                                                                   <  1:1483768/122‑1 (MQ=255)                                                                  ccAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCg                                                                  >  1:155496/1‑139 (MQ=255)                                                                  ccAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCg                                                                  >  2:1686605/1‑139 (MQ=255)                                                                        aaTGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCAt                                                                                                          >  2:703827/1‑93 (MQ=255)                                                                        aaTGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCAt                                                                                                          <  1:703827/93‑1 (MQ=255)                                                                          tGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTAt                                                                                                 >  2:1167580/1‑100 (MQ=255)                                                                          tGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTAt                                                                                                 <  1:1167580/100‑1 (MQ=255)                                                                          tGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGAc                                                          >  2:1239773/1‑139 (MQ=255)                                                                                aCAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTG‑TC‑‑CAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGc                                                 >  1:599976/1‑139 (MQ=255)                                                                                 cAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTG‑TC‑‑CAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCg                                                <  2:599976/139‑1 (MQ=255)                                                                                  aGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCcaa                                                                                                                                     >  2:319362/1‑56 (MQ=255)                                                                                  aGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCcaa                                                                                                                                     <  1:319362/56‑1 (MQ=255)                                                                                  aGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCgtg                                                                                       >  2:435659/1‑102 (MQ=255)                                                                                  aGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCgtg                                                                                       <  1:435659/102‑1 (MQ=255)                                                                                    cGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTgg                                                                                                                          >  1:1055389/1‑65 (MQ=255)                                                                                    cGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTgg                                                                                                                          <  2:1055389/65‑1 (MQ=255)                                                                                    cGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCAt                                                                                                          >  2:182221/1‑81 (MQ=255)                                                                                    cGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCAt                                                                                                          <  1:182221/81‑1 (MQ=255)                                                                                    cGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTg                                                  <  1:587323/137‑1 (MQ=255)                                                                                    cGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTg                                                  >  2:587323/1‑137 (MQ=255)                                                                                      gCAATATTCCGTCGCAGTGTACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCa                                                                           >  2:937791/1‑110 (MQ=255)                                                                                      gCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCa                                                                           <  1:937791/110‑1 (MQ=255)                                                                                                 tCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCAt                                                                                                          >  2:1536846/1‑68 (MQ=255)                                                                                                 tCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCAt                                                                                                          <  1:1536846/68‑1 (MQ=255)                                                                                                    cAGTATACTGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGa                                <  1:1686605/139‑1 (MQ=255)                                                                                                         taCTGAGTCACAGCTGGCGCAACTGATGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCa                           >  2:286078/1‑139 (MQ=255)                                                                                                            tGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCAt                                                                                                          >  2:648268/1‑57 (MQ=255)                                                                                                            tGAGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCAt                                                                                                          <  1:648268/57‑1 (MQ=255)                                                                                                              aGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATTGTGGTCGTGGTGGTTCTggta                                                                           <  2:1016955/86‑3 (MQ=255)                                                                                                              aGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCa                                                                           >  1:1016955/1‑86 (MQ=255)                                                                                                              aGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCg                                                                  >  1:67929/1‑95 (MQ=255)                                                                                                              aGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCg                                                                  <  2:67929/95‑1 (MQ=255)                                                                                                              aGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGaaa                                       <  2:64453/122‑1 (MQ=255)                                                                                                              aGTCACAGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGaaa                                       >  1:64453/1‑122 (MQ=255)                                                                                                                 cacaGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTAtgg                                                                                               <  1:1037919/63‑1 (MQ=255)                                                                                                                 cacaGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTAtgg                                                                                               >  2:1037919/1‑63 (MQ=255)                                                                                                                 cacaGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTtc                                                                     <  2:1394711/89‑1 (MQ=255)                                                                                                                 cacaGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTtc                                                                     >  1:1394711/1‑89 (MQ=255)                                                                                                                 cacaGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCAACGGCgaa                   >  1:881959/1‑139 (MQ=255)                                                                                                                 cacaGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCAACGGCgaa                   >  1:150129/1‑139 (MQ=255)                                                                                                                   caGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCgtg                                                                                       >  2:1279792/1‑69 (MQ=255)                                                                                                                   caGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCgtg                                                                                       <  1:1279792/69‑1 (MQ=255)                                                                                                                   caGCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGtt                                                                      >  1:981795/1‑86 (MQ=255)                                                                                                                   caGCTGGCGCAACTGGTGTCCAACAACCGTCTGCATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTGCTGGCATTGtt                                                                      <  2:981795/86‑1 (MQ=255)                                                                                                                     gCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTg                                                  <  2:563177/104‑1 (MQ=255)                                                                                                                     gCTGGCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTg                                                  >  1:563177/1‑104 (MQ=255)                                                                                                                        ggCGCAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCAACGGCGAAAGAAACg            <  1:1239773/139‑1 (MQ=255)                                                                                                                          cgcAACTGGTGTCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCAACGGCGAAAGAAACGcc          <  2:881959/139‑1 (MQ=255)                                                                                                                                  gtgtCCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCAACGGCGAAAGAAACGCCGTATGAAc  <  2:625382/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                       GCAGGCTGGCAGAAAGCGTTTAGCCCGGATGCGAAAGTCGGCTTCCTGGCCATTGCTAATAAGTTCCAGGCAATGATCGACAGCGGCAATATTCCGTCGCAGTATACTGAGTCACAGCTGGCGCAACTGGTGTTCAACAACCGTCTGGATGCCGGGTTAACCATCTTCTTTATGGTGGTCGTGGTGGTTCTGGCACTGTTCTCGATTAAGACGGCACTTGCGGCATTGAAAGATCCGAAGCCAACGGCGAAAGAAACGCCGTATGAAC  >  NC_000913/631679‑631946

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑