Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	922,366	C→T	*75* (TAG→TAA)	cspD ←	inhibitor of DNA replication, cold shock protein homolog

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	922,366	0	C	T	96.9%	192.5 / ‑2.3	64	*75* (TAG→TAA)	cspD	inhibitor of DNA replication, cold shock protein homolog
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (31/31);  total (32/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

CTGGTTACCCGCACGAAATGCGGCACGACTGGATCCAGTAGATGCTCTGGCACGAGAGTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGCTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGTTCTGTAACCATCCATCTGAATGGTGGAATA  >  NC_000913/922233‑922500                                                                                                                                      |                                                                                                                                        cTGGTTACCCGCACGAAATGCGGCACGACTGGATCCAGTAGATGCTCTGGCACGAGAGTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGc                                                                                                                                    >  2:834904/1‑139 (MQ=255)    gTTACCCGCACGAAATGCGGCACGACTGGATCCAGTAGATGCTCTGGCACGAGAGTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGAc                                                                                                                                 >  1:906620/1‑139 (MQ=255)    gTTACCCGCACGAAATGCGGCACGACTGGATCCAGTAGATGCTCTGGCACGAGAGTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGAc                                                                                                                                 >  2:909572/1‑139 (MQ=255)    gTTACCCGCACGAAATGCGGCACGACTGGATCCAGTAGATGCTCTGGCACGAGAGTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGAc                                                                                                                                 >  1:451759/1‑139 (MQ=255)                         aCGACTGGATCCAGTAGATGCTCTGGCACGAGAGTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACgga                                                                                                            <  1:1123873/139‑2 (MQ=255)                              tGGATCCAGTAGATGCTCTGGCACGAGAGTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACaa                                                                                                       <  1:909572/139‑1 (MQ=255)                                          aTGCTCTGGCACGAGAGTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGt                                                                                           >  1:1475131/1‑139 (MQ=255)                                               ctGGCACGAGAGTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTg                                                                                      >  2:1535222/1‑139 (MQ=255)                                               ctGGCACGAGAGTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTg                                                                                      <  2:451759/139‑1 (MQ=255)                                                     cGAGAGTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCtttt                                                                                <  2:1475131/139‑1 (MQ=255)                                                       agagTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACggg                                                                                                            <  2:483368/109‑1 (MQ=255)                                                       agagTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACggg                                                                                                            >  1:483368/1‑109 (MQ=255)                                                        gagTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACggg                                                                                                            >  1:1501717/1‑108 (MQ=255)                                                        gagTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACggg                                                                                                            <  2:1501717/108‑1 (MQ=255)                                                           tAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGcccc                                                                          <  1:834904/139‑1 (MQ=255)                                                            aaTTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAAt                                                                                                      <  2:1582930/110‑1 (MQ=255)                                                            aaTTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAAt                                                                                                      >  1:1582930/1‑110 (MQ=255)                                                                    agaTAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACa                                                                 >  1:759484/1‑139 (MQ=255)                                                                    agaTAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACa                                                                 >  1:46635/1‑139 (MQ=255)                                                                                  gCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCtg                                                                        >  2:43040/1‑118 (MQ=255)                                                                                  gCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCtg                                                                        <  1:43040/118‑1 (MQ=255)                                                                                  gCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGa                                                  <  2:906620/139‑1 (MQ=255)                                                                                       tCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTc                                             >  2:1538995/1‑139 (MQ=255)                                                                                             tGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCtt                                       >  1:619580/1‑139 (MQ=255)                                                                                             tGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGCTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAACGGGATTGTCCAGCt                                        >  2:247809/1‑139 (MQ=255)                                                                                                cATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTa                                    <  2:759484/139‑1 (MQ=255)                                                                                                 aTTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAg                                   <  1:880202/139‑1 (MQ=255)                                                                                                 aTTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAg                                   <  2:46635/139‑1 (MQ=255)                                                                                                     tGCCTTTAGGATGTACACAATGAGACAGCAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCtttt                                                                                >  1:1161027/1‑91 (MQ=255)                                                                                                     tGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCg                                                                                                                 <  1:756903/58‑1 (MQ=255)                                                                                                     tGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCg                                                                                                                 >  2:756903/1‑58 (MQ=255)                                                                                                     tGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCtttt                                                                                <  2:1161027/91‑1 (MQ=255)                                                                                                     tGCCTTTAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGtt                               <  1:1538995/139‑1 (MQ=255)                                                                                                         tttAGGATGTACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGTTCTGt                           >  1:330881/1‑139 (MQ=255)                                                                                                                  tACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACa                                                                 >  1:208950/1‑93 (MQ=255)                                                                                                                  tACACAATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACa                                                                 <  2:208950/93‑1 (MQ=255)                                                                                                                    cacaATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGc                                                                                                           >  2:350829/1‑49 (MQ=255)                                                                                                                    cacaATGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGc                                                                                                           <  1:350829/49‑1 (MQ=255)                                                                                                                       aaTGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACg                                                                                                              <  2:1313767/43‑1 (MQ=255)                                                                                                                       aaTGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACg                                                                                                              >  1:1313767/1‑43 (MQ=255)                                                                                                                       aaTGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGTTCTGTAACCATCCATCTGa             >  2:1522259/1‑139 (MQ=255)                                                                                                                        aTGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCg                                                                                                                 >  2:1019698/1‑39 (MQ=255)                                                                                                                        aTGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCg                                                                                                                 <  1:1019698/39‑1 (MQ=255)                                                                                                                        aTGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGc                                                                             >  1:1565309/1‑75 (MQ=255)                                                                                                                        aTGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGc                                                                             <  2:1565309/75‑1 (MQ=255)                                                                                                                        aTGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGa                                                        >  2:633726/1‑96 (MQ=255)                                                                                                                        aTGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGa                                                        <  1:633726/96‑1 (MQ=255)                                                                                                                        aTGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGTTCTGTAACCATCCATCTGaa            <  1:1535222/139‑1 (MQ=255)                                                                                                                         tGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGc                                                                             <  1:153087/74‑1 (MQ=255)                                                                                                                         tGAGACAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGc                                                                             >  2:153087/1‑74 (MQ=255)                                                                                                                         tGAGACAGAAGAGCTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAACGGGATTGTCCAGCTTTTAGCGTTCTGTAACCATCCATCTGaa            <  1:247809/139‑1 (MQ=255)                                                                                                                            gaCAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGtt                               <  2:1495287/116‑1 (MQ=255)                                                                                                                            gaCAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGtt                               >  1:1495287/1‑116 (MQ=255)                                                                                                                            gaCAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGTTCTGTAACCATCCATCTGaa            <  2:346749/135‑1 (MQ=255)                                                                                                                            gaCAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGTTCTGTAACCATCCATCTGaa            >  1:346749/1‑135 (MQ=255)                                                                                                                              cAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGa                                                  <  2:1702667/95‑1 (MQ=255)                                                                                                                              cAGAAGAGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGa                                                  >  1:1702667/1‑95 (MQ=255)                                                                                                                                 aagaGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCtggt                                                                      >  1:725599/1‑73 (MQ=255)                                                                                                                                 aagaGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCtggt                                                                      <  2:725599/73‑1 (MQ=255)                                                                                                                                 aagaGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGtt                               <  1:1150534/111‑1 (MQ=255)                                                                                                                                 aagaGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGTTCTGTAACCATCCATCTGAAtg          >  2:991556/1‑132 (MQ=255)                                                                                                                                 aagaGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGTTCTGTAACCATCCATCTGAAtg          <  1:991556/132‑1 (MQ=255)                                                                                                                                 aagaGTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTGAGCGtt                               >  2:1150534/1‑111 (MQ=255)                                                                                                                                  agagTTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGTTCTGTAACCATCCATCTGAATGGTGGaata  <  2:330881/139‑1 (MQ=255)                                                                                                                                      |                                                                                                                                        CTGGTTACCCGCACGAAATGCGGCACGACTGGATCCAGTAGATGCTCTGGCACGAGAGTAATTTTTGAGATAAAAATGCCAGCCGATCGGGCTGGCATTTTGCCTTTAGGATGTACACAATGAGACAGAAGAGCTATGCGACTGCCGCTTCTACTTCGACGGGCACAATAACACTGGCGTGATTGCCTTTTGGCCCCTGGTGGACATCAAACTGAAC‑GGATTGTCCAGCTTTTAGCGTTCTGTAACCATCCATCTGAATGGTGGAATA  >  NC_000913/922233‑922500

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: ‑