Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A25 F36 I0 R2 1302 104.9 4551290 96.3% 4382892 111.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 989,879:1 +C 6.3% coding (478/1203 nt) pncB ← nicotinate phosphoribosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913989,8791.C 6.3% 276.1 / 13.4 63coding (478/1203 nt)pncBnicotinate phosphoribosyltransferase
Reads supporting (aligned to +/- strand):  ref base . (29/30);  new base C (2/2);  total (31/32)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.25e-01

GGTGCCCACAAACCAGGATTCCTGTTGCAGACGCTTAACGATGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGAACTTCCCAGAGGATGACTTCACGCCACGGGCCGC  >  NC_000913/989754‑990022
                                                                                                                              |                                                                                                                                               
ggTGCCCACAAACCAGGATTCCTGTTGCAGACGCTTAACGATGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCAGCGGTTAA‑CGCCGAGAAGt                                                                                                                                      >  3:521445/1‑137 (MQ=255)
ggTGCCCACAAACCAGGATTCCTGTTGCAGACGCTTAACGATGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCAGCGGTTAA‑CGCCGAGAAGt                                                                                                                                      <  4:521445/137‑1 (MQ=255)
  tGCCCACAAACCAGGATTCCTGTTGCAGACGCTTAACGATGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCt                                                                                                                         <  3:259580/148‑1 (MQ=255)
                  ttCCTGTTGCAGACGCTTAACGATGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAGGTCg                                                                                                                                    >  3:71074/1‑121 (MQ=255)
                  ttCCTGTTGCAGACGCTTAACGATGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAGGTCg                                                                                                                                    <  4:71074/121‑1 (MQ=255)
                             gACGCTTAACGATGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCg                                                                                                                                            <  2:711642/102‑1 (MQ=255)
                             gACGCTTAACGATGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCg                                                                                                                                            >  1:711642/1‑102 (MQ=255)
                                 cTTAACGATGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGC‑GTTAA‑ccgcc                                                                                                                                            <  4:458439/97‑5 (MQ=255)
                                 cTTAACGATGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGC‑GTTAA‑ccgcc                                                                                                                                            >  3:458439/1‑93 (MQ=255)
                                         tGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTg                                                                                                    >  4:268482/1‑130 (MQ=255)
                                         tGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTg                                                                                                    <  3:268482/130‑1 (MQ=255)
                                            tttCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTaa                                                                                                                                                  >  4:225620/1‑82 (MQ=255)
                                            tttCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTaa                                                                                                                                                  <  3:225620/82‑1 (MQ=255)
                                                 tGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAAt                                                                                                                              <  4:130632/96‑1 (MQ=255)
                                                 tGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAAt                                                                                                                              >  3:130632/1‑96 (MQ=255)
                                                 tGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAg                                                                                                                   >  1:1030725/1‑107 (MQ=255)
                                                 tGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAg                                                                                                                   <  2:1030725/107‑1 (MQ=255)
                                                    aCTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCgaga                                                                                                                                         <  3:824149/82‑1 (MQ=255)
                                                    aCTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCgaga                                                                                                                                         >  4:824149/1‑82 (MQ=255)
                                                    aCTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGagc                                                                             >  1:661393/1‑142 (MQ=255)
                                                    aCTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGagc                                                                             <  2:661393/142‑1 (MQ=255)
                                                     cTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCgaga                                                                                                                                         >  4:743888/1‑81 (MQ=255)
                                                     cTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCgaga                                                                                                                                         <  3:743888/81‑1 (MQ=255)
                                                       tCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAAt                                                                                                                              >  2:417076/1‑90 (MQ=255)
                                                       tCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAAt                                                                                                                              <  1:417076/90‑1 (MQ=255)
                                                       tCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAg                                                                                                          <  3:176452/110‑1 (MQ=255)
                                                       tCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAg                                                                                                          >  4:176452/1‑110 (MQ=255)
                                                          cgAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCgg                                                                                         >  2:273720/1‑124 (MQ=255)
                                                          cgAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCgg                                                                                         <  1:273720/124‑1 (MQ=255)
                                                            agaAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTc                                                                                                                      <  1:933376/93‑1 (MQ=255)
                                                            agaAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTc                                                                                                                      >  2:933376/1‑93 (MQ=255)
                                                             gaAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGagcgat                                                                          >  2:780660/1‑136 (MQ=255)
                                                             gaAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGagcgat                                                                          <  1:780660/136‑1 (MQ=255)
                                                                 aaCGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTc                                                          >  2:469817/1‑148 (MQ=255)
                                                                       gACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGagcgatagcga                                                                     >  2:842659/1‑131 (MQ=255)
                                                                       gACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGagcgatagcga                                                                     <  1:842659/131‑1 (MQ=255)
                                                                        aCGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTg                                                      <  1:315396/145‑1 (MQ=255)
                                                                        aCGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTg                                                      >  2:315396/1‑145 (MQ=255)
                                                                           ggTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGagcgata                                                                         >  2:773835/1‑123 (MQ=255)
                                                                           ggTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGagcgata                                                                         <  1:773835/123‑1 (MQ=255)
                                                                                         tCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCgtg                                                                                                               >  2:67886/1‑71 (MQ=255)
                                                                                         tCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCgtg                                                                                                               <  1:67886/71‑1 (MQ=255)
                                                                                          cAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGAACt                                 >  4:429369/1‑148 (MQ=255)
                                                                                            gATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTAc                                                                >  1:107200/1‑115 (MQ=255)
                                                                                            gATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTAc                                                                <  2:107200/115‑1 (MQ=255)
                                                                                             aTGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATg                                                                   <  1:440487/111‑1 (MQ=255)
                                                                                             aTGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATg                                                                   >  2:440487/1‑111 (MQ=255)
                                                                                             aTGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGAACTTcc                              <  3:429369/148‑1 (MQ=255)
                                                                                                 aaGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGAACTTCCCaga                          <  1:469817/148‑1 (MQ=255)
                                                                                                    cgcgACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCAc                                                        <  3:54541/115‑1 (MQ=255)
                                                                                                    cgcgACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCAc                                                        >  4:54541/1‑115 (MQ=255)
                                                                                                              cAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCaa                                        <  2:199696/121‑1 (MQ=255)
                                                                                                              cAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCaa                                        >  1:199696/1‑121 (MQ=255)
                                                                                                              cAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGAACTTCCCAGAGGATGACTTCACg             >  2:703387/1‑148 (MQ=255)
                                                                                                                      ggcgTTAACCGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTc                                                          <  2:281476/93‑1 (MQ=255)
                                                                                                                      ggcgTTAACCGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTc                                                          <  4:498146/93‑1 (MQ=255)
                                                                                                                      ggcgTTAACCGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTc                                                          >  3:498146/4‑96 (MQ=255)
                                                                                                                      ggcgTTAACCGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTc                                                          >  1:281476/4‑96 (MQ=255)
                                                                                                                       cggTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCa                                                         >  1:649151/1‑95 (MQ=255)
                                                                                                                       cggTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCa                                                         <  2:649151/95‑1 (MQ=255)
                                                                                                                       cggTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGAACTTccc                             >  3:646267/1‑123 (MQ=255)
                                                                                                                       cggTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGAACTTccc                             <  4:646267/123‑1 (MQ=255)
                                                                                                                         gTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGAACTTCCCAGAGGATGACTTCACGCCACGGGCCGc  <  1:703387/148‑1 (MQ=255)
                                                                                                                          ttAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGAACTTCCCAGAgg                        >  3:592964/1‑125 (MQ=255)
                                                                                                                          ttAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGAACTTCCCAGAgg                        <  4:592964/125‑1 (MQ=255)
                                                                                                                           tAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGa                                    <  4:148753/112‑1 (MQ=255)
                                                                                                                           tAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGa                                    >  3:148753/1‑112 (MQ=255)
                                                                                                                              |                                                                                                                                               
GGTGCCCACAAACCAGGATTCCTGTTGCAGACGCTTAACGATGGTTTCTTGTACTTCGCGAGAAAAACGGCGACGGGTGCCAAAATCCATCAGATGGAAGCGCGACATATCAAGACCGGCGGTTAA‑CGCCGAGAAGTCGACTAATTTGCTTTCCAGCGTGTCGAGGGCTTGCGCAACGTCGGCCTGCGGTGAGCGATAGCGATGTACCATTTCACTGATAACCGCCAGCAAAGGAACTTCCCAGAGGATGACTTCACGCCACGGGCCGC  >  NC_000913/989754‑990022

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A