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 3,204,990 T→C 45.0% intergenic (‑78/‑129) ygiP ← / → ttdA predicted DNA‑binding transcriptional regulator/L‑tartrate dehydratase, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,204,9900TC45.0% 12.0 / 80.7 60intergenic (‑78/‑129)ygiP/ttdApredicted DNA‑binding transcriptional regulator/L‑tartrate dehydratase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (18/15);  new base C (18/9);  total (36/24)
Fisher's exact test for biased strand distribution p-value = 4.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.92e-01

ATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACA  >  W3110S.gb/3204921‑3205058
                                                                     |                                                                    
aTCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATattcatt                                                                     >  1:2940278/1‑71 (MQ=255)
aTCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATattcat                                                                      >  1:2468061/1‑70 (MQ=255)
aTCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATattcat                                                                      >  1:1047083/1‑70 (MQ=255)
          gtgATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTcg                                                           >  1:3609067/1‑71 (MQ=255)
              tAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGtt                                                       <  1:1687335/71‑1 (MQ=255)
               aaGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGtt                                                       >  1:1074734/1‑70 (MQ=255)
               aaGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGtt                                                       >  1:1410494/1‑70 (MQ=255)
               aaGCGCAGTGTATTTCGCAAAACATTGCCATTCCCCGCTCTGGCGCAATATTCACTCTTATTTTCGCGtt                                                       >  1:184662/1‑70 (MQ=255)
                aGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGa                                                     >  1:3191411/1‑71 (MQ=255)
                 gcgcAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGAt                                                    <  1:2276380/71‑1 (MQ=255)
                  cgcAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTAtt                                                               <  1:3470660/59‑1 (MQ=255)
                   gcAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGAtt                                                   <  1:2260586/70‑1 (MQ=255)
                      gtgtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACg                                               <  1:583133/71‑1 (MQ=255)
                      gtgtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACg                                               <  1:3675968/71‑1 (MQ=255)
                      gtgtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACg                                               <  1:2920316/71‑1 (MQ=255)
                      gtgtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACg                                               <  1:1185309/71‑1 (MQ=255)
                      gtgtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACg                                               <  1:3846199/71‑1 (MQ=255)
                       tgtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTAttt                                                              <  1:3230368/55‑1 (MQ=255)
                        gtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGa                                                     >  1:3083187/1‑63 (MQ=255)
                        gtATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGaa                                             >  1:1499033/1‑71 (MQ=255)
                           tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATattcatt                                                                     >  1:1148045/1‑44 (MQ=255)
                           tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCActct                                                                   >  1:3332595/1‑46 (MQ=255)
                           tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCActct                                                                   >  1:2690450/1‑46 (MQ=255)
                           tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTTGCGTTg                                                      <  1:321060/59‑1 (MQ=255)
                           tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGa                                                     >  1:1525926/1‑60 (MQ=255)
                           tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGa                                                     >  1:2934718/1‑60 (MQ=255)
                           tttCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGa                                                     >  1:1241073/1‑60 (MQ=255)
                             tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGt                                         >  1:264187/1‑70 (MQ=255)
                             tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGt                                         >  1:1849262/1‑70 (MQ=255)
                             tCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGt                                         >  1:1212342/1‑70 (MQ=255)
                             tCGCAAAACATTCCCATTCCCTCCTCTGGCGCAATATTCATACAAATTAACGCGTAGATTCACGAACTg                                          >  1:1850292/1‑69 (MQ=255)
                              cGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGtt                                        <  1:1663629/70‑1 (MQ=255)
                                cAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAAt                                     <  1:2109295/71‑1 (MQ=255)
                                cAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAAt                                     <  1:6274/71‑1 (MQ=255)
                                    aCATTGCCATTCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACa                                 <  1:1049087/71‑1 (MQ=255)
                                           cATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCAc                          <  1:318408/71‑1 (MQ=255)
                                           cATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCAc                          <  1:861835/71‑1 (MQ=255)
                                           cATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCAc                          <  1:1338995/71‑1 (MQ=255)
                                             ttCCCTGCTCTGGCGCAATATTCACTCTTATTTTCGCGtt                                                       <  1:432642/40‑1 (MQ=255)
                                              taccTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGAtt                                                   >  1:3901933/3‑43 (MQ=38)
                                               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCa                                                 >  1:425856/1‑44 (MQ=255)
                                               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCa                                                 >  1:2905603/1‑44 (MQ=255)
                                               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCa                                                 >  1:3080834/1‑44 (MQ=255)
                                               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGa                                              >  1:981018/1‑47 (MQ=255)
                                               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTaa                                      >  1:3253228/1‑55 (MQ=255)
                                               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTaa                                      >  1:3599423/1‑55 (MQ=255)
                                               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTAc                                  >  1:2198620/1‑59 (MQ=255)
                                               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACata                               >  1:1865564/1‑62 (MQ=255)
                                               cccTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTg                      >  1:920543/1‑71 (MQ=255)
                                               cccTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTg                      >  1:3547278/1‑71 (MQ=255)
                                               cccTGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTg                      >  1:3725887/1‑71 (MQ=255)
                                               cccTGCTCTGGCACAATATTCATTCTTATTTTCGCGTTGATTCACGa                                              >  1:1408216/1‑47 (MQ=255)
                                                  tGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGt                                         >  1:52322/1‑49 (MQ=255)
                                                  tGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGt                                         >  1:991937/1‑49 (MQ=255)
                                                  tGCTCTGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGt                                         >  1:2214278/1‑49 (MQ=255)
                                                   gCTCTGGCGAAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTaa                                      >  1:3654705/1‑51 (MQ=255)
                                                    ctctGGCGCAATATTCACTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCaa                  >  1:3173033/1‑70 (MQ=255)
                                                      ctGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAAt                                     >  1:2845110/1‑49 (MQ=255)
                                                          cgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAatat           <  1:612772/71‑1 (MQ=255)
                                                          cgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAatat           <  1:166253/71‑1 (MQ=255)
                                                          cgcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAatat           <  1:437549/71‑1 (MQ=255)
                                                           gcAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAatat           >  1:2002998/1‑70 (MQ=255)
                                                              atatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAata            >  1:3878915/1‑66 (MQ=255)
                                                              atatTCATTCTTATTTTCGCGTTCATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAata            >  1:1152730/1‑66 (MQ=255)
                                                               tatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTa                                   <  1:1971386/42‑1 (MQ=255)
                                                               tatTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAatat           <  1:2550216/66‑1 (MQ=255)
                                                                attcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACgg                        >  1:2990548/1‑52 (MQ=255)
                                                                attcactcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAAc      >  1:590572/1‑70 (MQ=255)
                                                                 ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATaaaa       >  1:732708/1‑68 (MQ=255)
                                                                 ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATaaaa       >  1:1278051/1‑68 (MQ=255)
                                                                 ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATaaaa       >  1:2792476/1‑68 (MQ=255)
                                                                 ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATaa         <  1:1038235/66‑1 (MQ=255)
                                                                 ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATaa         <  1:1932335/66‑1 (MQ=255)
                                                                 ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACca    >  1:2584012/1‑71 (MQ=255)
                                                                 ttcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACca    >  1:3443732/1‑71 (MQ=255)
                                                                 ttcactcTTATTTTCGCGTTGATTCACGAACTGTTAATTACata                               >  1:2529512/1‑44 (MQ=255)
                                                                 ttcactcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACca    >  1:1801649/1‑71 (MQ=255)
                                                                  tcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTgg                     >  1:767668/1‑53 (MQ=255)
                                                                  tcattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTgg                     >  1:1477485/1‑53 (MQ=255)
                                                                   cattcTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACcaca  >  1:2672692/1‑71 (MQ=255)
                                                                     |                                                                    
ATCCGCAGTTGTGATAAGCGCAGTGTATTTCGCAAAACATTGCCATTCCCTGCTCTGGCGCAATATTCATTCTTATTTTCGCGTTGATTCACGAACTGTTAATTACATATTCACGGTGGCAAAAAATATAAAACCACA  >  W3110S.gb/3204921‑3205058

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