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 F28 I2 R2 356 55.1 4139924 95.4% 3949487 63.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 2,688,036 T→C I43V (ATT→GTT)  yfhG ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,688,0360TC96.0% 253.7 / ‑0.5 75I43V (ATT→GTT) yfhGconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (0/3);  new base C (24/48);  total (24/51)
Fisher's exact test for biased strand distribution p-value = 5.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGCAATGCCAGA  >  W3110S.gb/2687970‑2688103
                                                                  |                                                                   
tagcTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt                                                                  <  1:757737/67‑1 (MQ=255)
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt                                                                  <  1:89735/70‑1 (MQ=255)
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt                                                                  <  1:72138/70‑1 (MQ=255)
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt                                                                  <  1:3726381/70‑1 (MQ=255)
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt                                                                  <  1:348565/70‑1 (MQ=255)
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt                                                                  <  1:307469/70‑1 (MQ=255)
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt                                                                  <  1:1025725/70‑1 (MQ=255)
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt                                                                  <  1:1503068/70‑1 (MQ=255)
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt                                                                  <  1:2571229/70‑1 (MQ=255)
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAActtt                                                                  <  1:2310334/70‑1 (MQ=255)
tACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGGCAGCCAGTTGATAAACCGGAActtt                                                                  <  1:1191587/70‑1 (MQ=255)
   cTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttct                                                              <  1:1042375/71‑1 (MQ=255)
    ttGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttctt                                                             >  1:872561/1‑71 (MQ=255)
    ttGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttctt                                                             >  1:79289/1‑71 (MQ=255)
    ttGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttctt                                                             >  1:445551/1‑71 (MQ=255)
    ttGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttct                                                              >  1:2664830/1‑70 (MQ=255)
      gCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttcttc                                                            <  1:1093041/70‑1 (MQ=255)
      gCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttcttc                                                            <  1:268663/70‑1 (MQ=255)
      gCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttcttc                                                            <  1:1482633/70‑1 (MQ=255)
      gCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttcttc                                                            <  1:521833/70‑1 (MQ=255)
      gCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttcttc                                                            <  1:2204841/70‑1 (MQ=255)
      gCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttcttc                                                            <  1:1982308/70‑1 (MQ=255)
      gCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttcttc                                                            <  1:1982492/70‑1 (MQ=255)
       cAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttcttc                                                            <  1:3042352/69‑1 (MQ=255)
       cAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttcttc                                                            <  1:541325/69‑1 (MQ=255)
            cccAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGc                                                     <  1:3794280/71‑1 (MQ=255)
            cccAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGc                                                     <  1:3789823/71‑1 (MQ=255)
            cccAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGc                                                     <  1:1284988/71‑1 (MQ=255)
            cccAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGc                                                     <  1:1976512/71‑1 (MQ=255)
             ccAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGc                                                     <  1:1154656/70‑1 (MQ=255)
             ccAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGAT‑AACCGGAACTTTTTCTTCTGCTGGCGt                                                   <  1:1562622/71‑1 (MQ=255)
              cAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAGCTTTTTCTTCTGCTGGCGt                                                   <  1:534628/71‑1 (MQ=255)
              cAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGt                                                   <  1:2343146/71‑1 (MQ=255)
               aGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTa                                                  <  1:3797562/71‑1 (MQ=255)
               aGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTa                                                  <  1:1449183/71‑1 (MQ=255)
               aGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTa                                                  <  1:185248/71‑1 (MQ=255)
                      gCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAAtgg                                           >  1:2205688/1‑71 (MQ=255)
                      gCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAAtg                                            >  1:559579/1‑70 (MQ=255)
                               aGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAAtggctg                                        <  1:3765106/65‑1 (MQ=255)
                               aGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAAtggctg                                        <  1:3720327/65‑1 (MQ=255)
                               aGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTAt                                  <  1:3916039/71‑1 (MQ=255)
                                 tAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttct                                                              <  1:2660585/41‑1 (MQ=255)
                                 tAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttct                                                              <  1:313214/41‑1 (MQ=255)
                                 tAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttct                                                              <  1:273821/41‑1 (MQ=255)
                                 tAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttct                                                              <  1:3582712/41‑1 (MQ=255)
                                 tAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttct                                                              <  1:2509114/41‑1 (MQ=255)
                                 tAGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAAtggctggc                                      >  1:1225607/1‑65 (MQ=255)
                                  aGAAAGATAGTCAGCCAGTTGATAAACCGGAACTTTttct                                                              <  1:2053040/40‑1 (MQ=255)
                                    aaaGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGa                             <  1:1825230/71‑1 (MQ=255)
                                    aaaGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGa                             <  1:3988709/71‑1 (MQ=255)
                                    aaaGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGa                             <  1:1709923/71‑1 (MQ=255)
                                    aaaGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGa                             <  1:1705177/71‑1 (MQ=255)
                                    aaaGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGa                             <  1:683320/71‑1 (MQ=255)
                                     aaGATAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGa                             <  1:2529095/70‑1 (MQ=255)
                                        aTAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCt                         >  1:3971812/1‑71 (MQ=255)
                                        aTAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCt                         >  1:3373293/1‑71 (MQ=255)
                                        aTAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCt                         >  1:2775243/1‑71 (MQ=255)
                                        aTAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCt                         >  1:473670/1‑71 (MQ=255)
                                        aTAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCt                         >  1:695237/1‑71 (MQ=255)
                                        aTAGTCAGCCAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCt                         >  1:3725595/1‑71 (MQ=255)
                                                 cAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAAc                >  1:2958737/1‑71 (MQ=255)
                                                 cAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAAc                <  1:761574/71‑1 (MQ=255)
                                                 cAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAAc                >  1:1892884/1‑71 (MQ=255)
                                                 cAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAAc                >  1:777480/1‑71 (MQ=255)
                                                 cAGTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAAc                >  1:2094258/1‑71 (MQ=255)
                                                   gTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGa                             <  1:3190844/56‑1 (MQ=255)
                                                   gTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGa                             <  1:1913011/56‑1 (MQ=255)
                                                   gTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGa                             <  1:2543820/56‑1 (MQ=255)
                                                   gTTGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGa                             <  1:4094778/56‑1 (MQ=255)
                                                     tGATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAg            >  1:103554/1‑71 (MQ=255)
                                                      gATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAg            >  1:2584236/1‑70 (MQ=255)
                                                      gATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAg            >  1:2951402/1‑70 (MQ=255)
                                                      gATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAg            >  1:1140629/1‑70 (MQ=255)
                                                      gATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAg            >  1:1609564/1‑70 (MQ=255)
                                                      gATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAg            >  1:1853146/1‑70 (MQ=255)
                                                      gATAAACCGGAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAg            >  1:1389552/1‑70 (MQ=255)
                                                       aTAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGc           <  1:1934799/70‑1 (MQ=255)
                                                       aTAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGc           <  1:1478986/70‑1 (MQ=255)
                                                       aTAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGc           <  1:3153660/70‑1 (MQ=255)
                                                               gAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGCAATGCCAGa  <  1:3109278/71‑1 (MQ=255)
                                                               gAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGCAATGCCAGa  <  1:509580/71‑1 (MQ=255)
                                                               gAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGCAATGCCAGa  <  1:3711317/71‑1 (MQ=255)
                                                               gAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGCAATGCCAGa  <  1:164128/71‑1 (MQ=255)
                                                               gAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGCAATGCCAGa  <  1:2322398/71‑1 (MQ=255)
                                                               gAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGCAATGCCAGa  <  1:1803584/71‑1 (MQ=255)
                                                               gAACTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGCAATGCCAGa  <  1:165811/71‑1 (MQ=255)
                                                                  |                                                                   
TACCTTGCAGCGCCCAGATGTCGCTACATTCAGTAGAAAGATAGTCAGCCAGTTGATAAACCGGAATTTTTTCTTCTGCTGGCGTATCAATGGCTGGCTTATTGTGATTCTGCACGCAACCCAGCAATGCCAGA  >  W3110S.gb/2687970‑2688103

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A