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
A1 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 2,611,108 T→C 13.0% F185L (TTC→CTC)  hyfR → DNA‑binding transcriptional activator, formate sensing

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,611,1080TC13.0% 258.5 / 28.1 100F185L (TTC→CTC) hyfRDNA‑binding transcriptional activator, formate sensing
Reads supporting (aligned to +/- strand):  ref base T (46/41);  new base C (6/7);  total (52/48)
Fisher's exact test for biased strand distribution p-value = 7.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.10e-01

Only 100 of 107 total aligned reads displayed.

ATGCAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTGTGGTG  >  W3110S.gb/2611040‑2611175
                                                                    |                                                                   
aTGCAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCAtttttt                                                                    <  1:2384361/70‑1 (MQ=255)
aTGCAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTc                                                                   >  1:4486573/1‑71 (MQ=255)
aTGCAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTc                                                                   <  1:2785649/71‑1 (MQ=255)
 tGCAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCg                                                                  <  1:171003/71‑1 (MQ=255)
   cAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCgg                                                                 >  1:532853/1‑70 (MQ=255)
   cAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCgg                                                                 <  1:2827039/70‑1 (MQ=255)
   cAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGt                                                                >  1:3990527/1‑71 (MQ=255)
   cAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGt                                                                <  1:378757/71‑1 (MQ=255)
     gTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCt                                                              <  1:4376955/71‑1 (MQ=255)
     gTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGt                                                                <  1:48497/69‑1 (MQ=255)
        cTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTc                                                               >  1:1592840/1‑67 (MQ=255)
        cTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTgg                                                            >  1:2033971/1‑70 (MQ=255)
        cTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTgg                                                            <  1:3380963/70‑1 (MQ=255)
          gTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCtt                                                         >  1:1140568/1‑71 (MQ=255)
           tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCtt                                                         <  1:321594/70‑1 (MQ=255)
           tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCtt                                                         <  1:1513970/70‑1 (MQ=255)
           tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCtt                                                         <  1:3346596/70‑1 (MQ=255)
           tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCtt                                                         <  1:3758642/70‑1 (MQ=255)
           tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCtt                                                         <  1:1287853/70‑1 (MQ=255)
           tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCtt                                                         <  1:4595205/70‑1 (MQ=255)
           tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCtt                                                         >  1:3068494/1‑70 (MQ=255)
           tCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCt                                                          <  1:1096813/69‑1 (MQ=255)
             acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCAttttt                                                                     >  1:1806512/1‑56 (MQ=255)
             acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGt                                                                >  1:4458401/1‑61 (MQ=255)
             acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcag                                                      >  1:1378662/1‑71 (MQ=255)
             acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcag                                                      >  1:1302330/1‑71 (MQ=255)
             acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcag                                                      <  1:1237081/71‑1 (MQ=255)
             acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcag                                                      <  1:4477032/71‑1 (MQ=255)
             acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcag                                                      <  1:4471677/71‑1 (MQ=255)
             acaTCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcag                                                      <  1:4036523/71‑1 (MQ=255)
                  ttGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGt                                                                >  1:2516881/1‑56 (MQ=255)
                    gATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag                                                  <  1:3246725/68‑1 (MQ=255)
                    gATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag                                                  <  1:3684943/68‑1 (MQ=255)
                    gATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTcagtcagt                                                 <  1:3636893/69‑1 (MQ=255)
                    gATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTa                                                <  1:1470591/70‑1 (MQ=255)
                     aTCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGt                                                                >  1:1585442/1‑53 (MQ=255)
                     aTCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTAt                                               <  1:2571540/70‑1 (MQ=255)
                        tcGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGc                                                           <  1:2710340/55‑1 (MQ=255)
                          gacgaTCTGATCGCTGCCGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACt                                         >  1:3112764/1‑71 (MQ=255)
                          gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCAtttttt                                                                    >  1:4274483/1‑44 (MQ=255)
                          gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATgg                                             >  1:2712712/1‑67 (MQ=255)
                          gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGt                                            <  1:4048359/68‑1 (MQ=255)
                          gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGt                                            <  1:863050/68‑1 (MQ=255)
                          gacgaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACt                                         >  1:2726128/1‑71 (MQ=255)
                             gaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGc                                                           <  1:477593/50‑1 (MQ=255)
                             gaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtca                                                   >  1:2206104/1‑58 (MQ=255)
                             gaTCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtca                                                   >  1:3026753/1‑58 (MQ=255)
                              aTCTGATCGCTGACGTCGCTCGTGAGATCCATCAtttttt                                                                    <  1:617997/40‑1 (MQ=255)
                              aTCTGATCGCTGACGTCGCTCGTGAGATCCATCAtttttt                                                                    <  1:3420027/40‑1 (MQ=255)
                               tCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGc                                     >  1:2515667/1‑70 (MQ=255)
                                cTGATCGCTGACGTCTCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtca                                                       >  1:1883378/1‑51 (MQ=255)
                                cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtca                                                       >  1:4375239/1‑51 (MQ=255)
                                cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTg                                        >  1:930972/1‑66 (MQ=255)
                                cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTg                                        >  1:1915734/1‑66 (MQ=255)
                                cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGa                                   >  1:509681/1‑71 (MQ=255)
                                cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGa                                   >  1:2631525/1‑71 (MQ=255)
                                cTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGa                                   >  1:2776700/1‑71 (MQ=255)
                                   aTCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTa                                                >  1:1275774/1‑55 (MQ=255)
                                   aTCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGatca                                >  1:1919418/1‑71 (MQ=255)
                                   aTCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGat                                  <  1:365643/69‑1 (MQ=255)
                                   aTCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGat                                  >  1:237182/1‑69 (MQ=255)
                                   aTCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTtc                                                        <  1:2050631/47‑1 (MQ=255)
                                    tCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtcag                                                  <  1:1244292/52‑1 (MQ=255)
                                    tCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGt                                            >  1:3480080/1‑58 (MQ=255)
                                    tCGCTGACGTCGCTCGTGAGATCCATCATTTTCTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGatcat                               >  1:226397/1‑71 (MQ=255)
                                         gACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtca                                                       >  1:599238/1‑42 (MQ=255)
                                         gACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtca                                                       >  1:12786/1‑42 (MQ=255)
                                         gACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTAc                                          >  1:1212118/1‑55 (MQ=255)
                                          aCGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGa                            >  1:4258498/1‑68 (MQ=255)
                                          aCGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAg                         <  1:1761381/71‑1 (MQ=255)
                                          aCGTCGCTCGTGAGATCAATCATTTTCTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAg                         <  1:2042432/71‑1 (MQ=255)
                                           cGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGa                        <  1:3398848/71‑1 (MQ=255)
                                               gCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtca                                                   >  1:4561932/1‑40 (MQ=255)
                                               gCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtca                                                   >  1:21188/1‑40 (MQ=255)
                                               gCTCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtca                                                   >  1:1314160/1‑40 (MQ=255)
                                               gCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTa                                           >  1:675441/1‑48 (MQ=255)
                                               gCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTAc                                          >  1:930699/1‑49 (MQ=255)
                                               gCTCGTGAGATCCATCATTTTCTCGGTCTGGCTtca                                                       >  1:90265/1‑36 (MQ=255)
                                                cTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACgag                   <  1:2251146/71‑1 (MQ=255)
                                                 tCGTGAGATCCATCATTTTTTCGGTCTGGCTtcagtca                                                   <  1:3486561/38‑1 (MQ=255)
                                                   gTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACgag                   <  1:3158210/68‑1 (MQ=255)
                                                   gTGAGATCCATCATTTTCTCGGTCTGGCTTCAGTCAGTa                                                >  1:4215709/1‑39 (MQ=255)
                                                     gagaTCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTa                                           <  1:3416505/42‑1 (MQ=255)
                                                        aTCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGaa                       >  1:1159679/1‑59 (MQ=255)
                                                        aTCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGt               <  1:652574/67‑1 (MQ=255)
                                                        aTCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAg           >  1:862079/1‑71 (MQ=255)
                                                          ccATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGat                                  <  1:689400/46‑1 (MQ=255)
                                                          ccATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAAc                      >  1:4511917/1‑58 (MQ=255)
                                                          acatcatTTTCTCGGTCTGGCTTCAGACAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCac           >  1:3155111/2‑68 (MQ=255)
                                                           catcatTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGcc         <  1:208221/70‑1 (MQ=255)
                                                            atcatTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCtg       <  1:4502441/71‑1 (MQ=255)
                                                            atcatTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCtg       <  1:2457631/71‑1 (MQ=255)
                                                             tcatTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGa                        <  1:2009281/53‑1 (MQ=255)
                                                             tcatTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGa                        <  1:170702/53‑1 (MQ=255)
                                                             tcatTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCtgt      <  1:4197913/71‑1 (MQ=255)
                                                              catTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCtgtg     >  1:2172104/1‑71 (MQ=255)
                                                              catTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCtgtg     >  1:2912328/1‑71 (MQ=255)
                                                               atTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTgtgg    >  1:3037342/1‑71 (MQ=255)
                                                                  ttttCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTgtggtg  >  1:3463742/1‑70 (MQ=255)
                                                                  ttttCCGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTgtggtg  <  1:225623/70‑1 (MQ=255)
                                                                    |                                                                   
ATGCAGTGCTGTCACATCTTGATCTCGACGATCTGATCGCTGACGTCGCTCGTGAGATCCATCATTTTTTCGGTCTGGCTTCAGTCAGTATGGTACTGGGCGATCATCGAAAGAACGAGAAGTTCAGCCTGTGGTG  >  W3110S.gb/2611040‑2611175

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A