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 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,633,778 T→C 22.2% C97C (TGT→TGC)  yigG → predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,633,7780TC22.2% 156.2 / 46.0 81C97C (TGT→TGC) yigGpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base T (24/39);  new base C (9/9);  total (33/48)
Fisher's exact test for biased strand distribution p-value = 4.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.65e-01

ATGTTTTTGGTACATTAGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATGCTTGC  >  W3110S.gb/3633711‑3633843
                                                                   |                                                                 
aTGTTTTTGGTACATTAGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGtt                                                                  >  1:1423617/1‑69 (MQ=255)
                aGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCgatga                                                >  1:3098846/1‑71 (MQ=255)
                aGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCgatga                                                >  1:3103576/1‑71 (MQ=255)
                aGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCgatga                                                >  1:151596/1‑71 (MQ=255)
                     tatataTCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGc                                                             <  1:3025368/53‑1 (MQ=255)
                     tatataTCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGc                                                             <  1:3014295/53‑1 (MQ=255)
                     tatataTCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGc                                                             <  1:2112234/53‑1 (MQ=255)
                     tatataTCATCTCTATCATCACAATGATACCCGAAGATTTTGCCTGTTCAGGc                                                             <  1:3213101/53‑1 (MQ=255)
                       tatatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCaa                                                           >  1:3637448/1‑53 (MQ=255)
                       tatatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAAt                                                          >  1:3755146/1‑54 (MQ=255)
                       tatatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGAttttttt                                         >  1:4052915/1‑71 (MQ=255)
                       tatatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGAttttttt                                         >  1:1525374/1‑71 (MQ=255)
                       tatatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGAttttt                                           >  1:3020365/1‑69 (MQ=255)
                       tatatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGAttttttt                                         >  1:3699876/1‑71 (MQ=255)
                       tatatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGAtttttt                                          >  1:2865025/1‑70 (MQ=255)
                       tatatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGAtttttt                                          >  1:1989108/1‑70 (MQ=255)
                         tatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGa                                       >  1:29354/1‑71 (MQ=255)
                         tatCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTAGATGATTTTTTTGa                                       >  1:2381784/1‑71 (MQ=255)
                          atcatcTCTATCATCACAATGATAGCCGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGAt                                      >  1:2155149/1‑71 (MQ=255)
                           tcatcTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGAtttt                                            <  1:1226611/64‑1 (MQ=255)
                           tcatcTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGAtt                                     >  1:1747172/1‑71 (MQ=255)
                           tcatcTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGAt                                      <  1:710501/70‑1 (MQ=255)
                           tcatcTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGAt                                      <  1:4030245/70‑1 (MQ=255)
                                tctATCGTCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTa                                >  1:525853/1‑71 (MQ=255)
                                tctATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTa                                >  1:2764340/1‑71 (MQ=255)
                                tctATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTa                                >  1:4029064/1‑71 (MQ=255)
                                  tATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGt                                  <  1:3946982/67‑1 (MQ=255)
                                  tATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGt                                  <  1:4006902/67‑1 (MQ=255)
                                   atcatcACAATGATAGCCGAAGATTTTGCCTGCTCAGGc                                                             <  1:639849/39‑1 (MQ=255)
                                   atcatcACAATGATAGCCGAAGATTTTGCCTGCTCAGGc                                                             <  1:209978/39‑1 (MQ=255)
                                    tcatcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAtttt                            <  1:2240992/71‑1 (MQ=255)
                                    tcatcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAt                               <  1:2724394/68‑1 (MQ=255)
                                      atcaCAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTc                          >  1:2128647/1‑71 (MQ=255)
                                      atcaCAATGATAGCCGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTc                          >  1:3797784/1‑71 (MQ=255)
                                        cacaATGATAGCCGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCa                        >  1:2954946/1‑71 (MQ=255)
                                             tGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACtt                     <  1:2085505/69‑1 (MQ=255)
                                             tGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACtt                     <  1:963778/69‑1 (MQ=255)
                                               aTAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 <  1:2892080/71‑1 (MQ=255)
                                               aTAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 <  1:1047330/71‑1 (MQ=255)
                                               aTAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 >  1:413138/1‑71 (MQ=255)
                                               aTAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 <  1:991912/71‑1 (MQ=255)
                                               aTAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 <  1:1057580/71‑1 (MQ=255)
                                               aTAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 <  1:2874476/71‑1 (MQ=255)
                                               aTAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 <  1:1511967/71‑1 (MQ=255)
                                               aTAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 >  1:1385610/1‑71 (MQ=255)
                                               aTAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 <  1:2887422/71‑1 (MQ=255)
                                                tAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGAttttttt                                         <  1:310489/46‑1 (MQ=255)
                                                tAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGAttttttt                                         <  1:1693879/46‑1 (MQ=255)
                                                tAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 <  1:1463582/70‑1 (MQ=255)
                                                tAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 <  1:2688250/70‑1 (MQ=255)
                                                tAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 <  1:254397/70‑1 (MQ=255)
                                                tAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGt                <  1:3489967/71‑1 (MQ=255)
                                                tAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCAACTTTCAg                 <  1:1402131/70‑1 (MQ=255)
                                                tAGCCGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTg                                   <  1:23804/52‑1 (MQ=255)
                                                 aGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTa               >  1:3945624/1‑71 (MQ=255)
                                                 aGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTa               >  1:3945622/1‑71 (MQ=255)
                                                  gCCGAAGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTAt              <  1:138946/71‑1 (MQ=255)
                                                     gAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt           <  1:3844669/71‑1 (MQ=255)
                                                     gAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt           <  1:3349739/71‑1 (MQ=255)
                                                     gAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt           <  1:3222227/71‑1 (MQ=255)
                                                     gAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt           <  1:2723305/71‑1 (MQ=255)
                                                     gAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt           <  1:806658/71‑1 (MQ=255)
                                                     gAAGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt           <  1:2593936/71‑1 (MQ=255)
                                                      aaGATTTTGCCTGTTCAGGCAATGGTTCGATGAttttttt                                         <  1:2315714/40‑1 (MQ=255)
                                                      aaGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTa                                <  1:980693/49‑1 (MQ=255)
                                                      aaGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt           <  1:1905290/70‑1 (MQ=255)
                                                      aaGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt           <  1:1305168/70‑1 (MQ=255)
                                                      aaGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt           <  1:2762772/70‑1 (MQ=255)
                                                      aaGATTTTGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCt           <  1:2859377/70‑1 (MQ=255)
                                                        gATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAAt        <  1:565976/71‑1 (MQ=255)
                                                        gATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAAt        <  1:2662036/71‑1 (MQ=255)
                                                           tttGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATGCt     >  1:2281675/1‑71 (MQ=255)
                                                           tttGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATGCt     >  1:4021281/1‑71 (MQ=255)
                                                           tttGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATGCt     >  1:3378326/1‑71 (MQ=255)
                                                           tttGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATGCt     >  1:494673/1‑71 (MQ=255)
                                                           tttGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCAc                       >  1:3810856/1‑53 (MQ=255)
                                                           tttGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCAc                       >  1:2341960/1‑53 (MQ=255)
                                                           tttGCCTGCTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCAc                       >  1:3201872/1‑53 (MQ=255)
                                                            ttGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATGCtt    >  1:2884495/1‑71 (MQ=255)
                                                               ccTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATGCTTGc  <  1:3792151/70‑1 (MQ=255)
                                                                  gTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTAttt                             <  1:3188169/40‑1 (MQ=255)
                                                                  gTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAg                 <  1:1860191/52‑1 (MQ=255)
                                                                   |                                                                 
ATGTTTTTGGTACATTAGCAGTATATATCATCTCTATCATCACAATGATAGCCGAAGATTTTGCCTGTTCAGGCAATGGTTCGATGATTTTTTTGATTTGTTATTTTTCCACTTTCAGTATGCTAATGCTTGC  >  W3110S.gb/3633711‑3633843

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