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
A2 F60 I1 R1 15 55.1 2015454 99.1% 1997314 138.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,334,528 G→A G144G (GGC→GGT)  yfaT ← DUF1175 domain‑containing protein YfaT

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,334,5280GA96.4% 167.2 / ‑1.1 55G144G (GGC→GGT) yfaTDUF1175 domain‑containing protein YfaT
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base A (29/24);  total (30/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.41e-01

GTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCGGTTTTCCCGTTCCCCTGATTCCAGTTTT  >  NC_000913/2334395‑2334661
                                                                                                                                     |                                                                                                                                     
gTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGa                                                                                                                                 >  1:174492/1‑140 (MQ=255)
   tCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCg                                                                                                                              >  2:173245/1‑140 (MQ=255)
       tCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGaaaa                                                                                                                          >  1:32330/1‑140 (MQ=255)
         gggTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGaaaaaa                                                                                                                        >  2:784506/1‑140 (MQ=255)
           gtgtCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAAt                                                                                                                      >  2:870046/1‑140 (MQ=255)
              tCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCat                                                                                                                   >  1:318335/1‑140 (MQ=255)
                   ccATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGc                                                                                                              >  2:508567/1‑140 (MQ=255)
                      tGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAg                                                                                                           >  1:592433/1‑140 (MQ=255)
                          aTAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAg                                                                                                       >  1:184157/1‑140 (MQ=255)
                             aGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAgcgc                                                                                                    <  2:174492/140‑1 (MQ=255)
                                    gCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGttt                                                                                             <  1:870046/140‑1 (MQ=255)
                                     cAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTa                                                                                            >  1:282010/1‑140 (MQ=255)
                                       gactgactGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATg                                                                                          >  1:407784/1‑140 (MQ=255)
                                         ctgactgCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTc                                                                                        <  2:318335/140‑1 (MQ=255)
                                         ctgactgCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTc                                                                                        <  1:718942/140‑1 (MQ=255)
                                           gactgCGCACATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCt                                                                                      <  2:373424/140‑1 (MQ=255)
                                            actgCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGtt                                                                                              >  1:171033/1‑131 (MQ=255)
                                            actgCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGtt                                                                                              <  2:171033/131‑1 (MQ=255)
                                                cgcgcATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCa                                                                                 <  1:862900/140‑1 (MQ=255)
                                                 gcgcATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCaa                                                                                <  2:288053/140‑1 (MQ=255)
                                                 gcgcATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCaa                                                                                <  1:578682/140‑1 (MQ=255)
                                                    cATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATaa                                                                             >  1:157773/1‑140 (MQ=255)
                                                       tCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACt                                                                          <  2:592433/140‑1 (MQ=255)
                                                         cGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTgg                                                                        <  2:590536/140‑1 (MQ=255)
                                                            tGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtg                                                                     <  2:282010/140‑1 (MQ=255)
                                                              tCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCtgtt                                                                   >  2:114391/1‑140 (MQ=255)
                                                               cAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACt                                                                          <  2:97469/132‑1 (MQ=255)
                                                               cAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACt                                                                          >  1:97469/1‑132 (MQ=255)
                                                                 gTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGTCAATAAACTGGCTGTTGTa                                                                <  2:407784/140‑1 (MQ=255)
                                                                 gTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCGGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGGTTATGTCCTGGCCAATAAACTGGCTGTTGTa                                                                <  2:961881/140‑1 (MQ=255)
                                                                        tGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATc                                                         >  2:268753/1‑140 (MQ=255)
                                                                            gcTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAt                                                     >  1:767020/1‑140 (MQ=255)
                                                                            gcTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAAt                                                     >  1:549051/1‑140 (MQ=255)
                                                                               tCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTaa                                                  >  2:134484/1‑140 (MQ=255)
                                                                                ccGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCATGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAAt                                                 <  1:49661/140‑1 (MQ=255)
                                                                                    tgtgGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATcgcg                                             <  2:184157/140‑1 (MQ=255)
                                                                                    tgtgGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATcgcg                                             <  2:32330/140‑1 (MQ=255)
                                                                                         tAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTcac                                        >  2:18931/1‑140 (MQ=255)
                                                                                            aTGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATa                                     <  1:395156/140‑1 (MQ=255)
                                                                                            aTGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATa                                     >  2:2398/1‑140 (MQ=255)
                                                                                            aTGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATa                                     >  1:948299/1‑140 (MQ=255)
                                                                                                cGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATcgc                                              >  1:560594/1‑127 (MQ=255)
                                                                                                cGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATcgc                                              <  2:560594/127‑1 (MQ=255)
                                                                                                cGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAgggg                                 <  1:173245/140‑1 (MQ=255)
                                                                                                   aaCGCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCg                              >  1:609672/1‑140 (MQ=255)
                                                                                                      gCCCCATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCGGtt                           >  1:138355/1‑140 (MQ=255)
                                                                                                         ccATCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCGGTTTTc                        <  2:948299/140‑1 (MQ=255)
                                                                                                           aTCCAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCACCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCGGTTTTccc                      >  2:328228/1‑140 (MQ=255)
                                                                                                            tCCAGACCATTAAGTGCTGGGCAGCACCCTGATCGAAAAAAACCATATCGCCACGCAGCGCCTGGCTTATGTCCTGTCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCGGTTTTTCCg                     >  2:160569/1‑140 (MQ=255)
                                                                                                              cAGACCATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCGGTTTTCCCGtt                   <  2:941684/140‑1 (MQ=255)
                                                                                                                   cATTAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCGGTTTTCCCGTTCCCCt              <  1:268753/140‑1 (MQ=255)
                                                                                                                   cATGAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCGGTTTTCCCGTTCCCCt              <  2:286787/140‑1 (MQ=255)
                                                                                                                      tAAGTGCTGGGCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCGGTTTTCCCGTTCCCCTGAt           >  1:561063/1‑140 (MQ=255)
                                                                                                                               ggCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCGGTTTTCCCGTTCCCCTGATTCCAGtttt  >  2:328804/1‑140 (MQ=255)
                                                                                                                               ggCATCACCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCGGTTTTCCCGTTCCCCTGATTCCAGtttt  >  1:165943/1‑140 (MQ=255)
                                                                                                                                     |                                                                                                                                     
GTATCCATCGGGTGTCCTTCCATGTCATAAGTTGTTGCAGACTGACTGCGCGCATTCCGTTGTCAGTTTTCGTGGCGCTTCCGGTGTGGTAGATGACGTAACGCCCCATCCAGACCATTAAGTGCTGGGCATCGCCCTGATCGAAAAAAATCATATCGCCAGGCAGCGCCTGGTTTATGTCCTGGCCAATAAACTGGCTGTTGTACTGAATCAAATTAATCGCGGTCACATAGGGGCCGGTTTTCCCGTTCCCCTGATTCCAGTTTT  >  NC_000913/2334395‑2334661

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A