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
A5 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,915,033 T→C 12.8% intergenic (+29/‑66) ysaB → / → glyQ hypothetical protein/glycine tRNA synthetase, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,915,0330TC12.8% 203.0 / 21.1 78intergenic (+29/‑66)ysaB/glyQhypothetical protein/glycine tRNA synthetase, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (32/36);  new base C (4/6);  total (36/42)
Fisher's exact test for biased strand distribution p-value = 7.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.96e-01

TTGACGCGGATGGCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCACACGTATCCAGCACGAAATAATATGC  >  W3110S.gb/3914964‑3915102
                                                                     |                                                                     
ttGACGCGGATGGCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGtat                                                                       <  1:2498198/70‑1 (MQ=255)
   aCGCGGATGGCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATc                                                                    <  1:3020841/70‑1 (MQ=255)
   aCGCGGATGGCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTACATc                                                                    <  1:2266519/70‑1 (MQ=255)
    cgcgGATGGCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCtt                                                                  <  1:2974097/71‑1 (MQ=255)
    cgcgGATGGCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCtt                                                                  >  1:4125360/1‑71 (MQ=255)
    cgcgGATGGCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCtt                                                                  >  1:4120195/1‑71 (MQ=255)
      cgGATGGCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTtcc                                                                <  1:505551/71‑1 (MQ=255)
       ggATGGCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTtcca                                                               <  1:1685771/71‑1 (MQ=255)
       ggATGGCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTtcca                                                               >  1:2208076/1‑71 (MQ=255)
       ggATGGCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTtcca                                                               <  1:3949071/71‑1 (MQ=255)
            gCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAg                                                          <  1:4163553/71‑1 (MQ=255)
            gCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTACATCTtccatcca                                                           <  1:2102023/70‑1 (MQ=255)
              cATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTtcc                                                                <  1:1693318/63‑1 (MQ=255)
               aTTTTTTGCATCTTTCCATGCGTTAAGCCTTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCgg                                                       >  1:840226/1‑71 (MQ=255)
               aTTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCgg                                                       >  1:3845248/1‑71 (MQ=255)
               aTTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCgg                                                       <  1:1213083/71‑1 (MQ=255)
                ttttttGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTACATCTTCCATCCAGCggg                                                      <  1:2981695/71‑1 (MQ=255)
                 tttttGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCggg                                                      >  1:2089946/1‑70 (MQ=255)
                 tttttGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTACATCTTCCATCCAGCggg                                                      >  1:3540666/1‑70 (MQ=255)
                  ttttGCATCTTTCCATGCGTTAAGCCCTGTTTTTTCCCGTTTCGTACTGTATATCTtccatcca                                                           >  1:2409982/1‑64 (MQ=255)
                  ttttGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATc                                                                    >  1:3386274/1‑55 (MQ=255)
                   tttGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTtcca                                                               >  1:706760/1‑59 (MQ=255)
                     tGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGta                                                    >  1:181253/1‑68 (MQ=255)
                      gCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGc                                                         <  1:3936129/62‑1 (MQ=255)
                       cATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTg                                               <  1:3147065/71‑1 (MQ=255)
                       cATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTg                                               <  1:3200928/71‑1 (MQ=255)
                        aTCTTTCCATGCGTTAGGCCTTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGa                                              <  1:2580096/71‑1 (MQ=255)
                        aTCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGtat                                                   <  1:4281104/66‑1 (MQ=255)
                         tCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGtat                                                                       <  1:4198528/45‑1 (MQ=255)
                         tCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTtccatcc                                                            >  1:2250638/1‑56 (MQ=255)
                         tCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGAt                                             >  1:2137977/1‑71 (MQ=255)
                          cTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTATTGTATATCTTCAATCCAGCGGGTATACTGATc                                            >  1:644062/1‑71 (MQ=255)
                          cTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTatat                                                                     >  1:695364/1‑46 (MQ=255)
                          cTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATAc                                                 <  1:1684199/66‑1 (MQ=255)
                          cTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATc                                            >  1:721387/1‑71 (MQ=255)
                           tttCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCtt                                                                  >  1:4561659/1‑48 (MQ=255)
                           tttCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGtata                                                  <  1:4288539/64‑1 (MQ=255)
                            ttCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCgg                                                       >  1:1458285/1‑58 (MQ=255)
                            ttCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCgg                                                       >  1:1746025/1‑58 (MQ=255)
                             tCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGAt                                             <  1:2945413/67‑1 (MQ=255)
                             tCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTACATCTTCCATCCAGCGGGTATACTGATccc                                          <  1:3701804/70‑1 (MQ=255)
                               cATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTATTGTATATCTTCCATCCAGCGGGTATACTGATCcctt                                        <  1:4189132/70‑1 (MQ=255)
                               cATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCccttc                                       <  1:4367778/71‑1 (MQ=255)
                               cATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCccttc                                       <  1:2965747/71‑1 (MQ=255)
                               cATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCccttc                                       <  1:2190694/71‑1 (MQ=255)
                                aTGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCcctt                                        <  1:4187160/69‑1 (MQ=255)
                                   cGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCccttcctt                                    >  1:3962811/1‑70 (MQ=255)
                                    gTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCccttcctt                                    >  1:4149394/1‑69 (MQ=255)
                                     ttAAGCCCTGCTTTTTCCCGTTTCGTATTGTATATCTtccatcca                                                           <  1:980797/45‑1 (MQ=255)
                                     ttAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCgg                                                       <  1:3750040/49‑1 (MQ=255)
                                     ttAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTaa                                 <  1:2384387/71‑1 (MQ=255)
                                      tAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTaaa                                >  1:2062926/1‑71 (MQ=255)
                                       aaGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTaaa                                <  1:1373728/70‑1 (MQ=255)
                                       aaGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAAt                               >  1:347707/1‑71 (MQ=255)
                                          cccTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCca                            <  1:2171373/71‑1 (MQ=255)
                                          cccTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCca                            <  1:3126590/71‑1 (MQ=255)
                                           ccTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGta                                                    <  1:817097/46‑1 (MQ=255)
                                           ccTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCcac                           <  1:2565048/71‑1 (MQ=255)
                                            cTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCggg                                                      <  1:379539/43‑1 (MQ=255)
                                             tGCTTTTTCCCGTTTCGTATTGTATATCTTCCATCCAGCGGGTATACTGATc                                            <  1:659840/52‑1 (MQ=255)
                                             tGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACt                                                <  1:2438315/48‑1 (MQ=255)
                                             tGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCccttc                                       >  1:642646/1‑57 (MQ=255)
                                              gCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCcctt                                        >  1:841567/1‑55 (MQ=255)
                                              gCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCacac                         >  1:3335326/1‑70 (MQ=255)
                                               cTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGa                                              >  1:4281289/1‑48 (MQ=255)
                                                tttttCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGtata                                                  >  1:3653650/1‑43 (MQ=255)
                                                tttttCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCacac                         >  1:40379/1‑68 (MQ=255)
                                                  tttCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGtata                                                  >  1:3690942/1‑41 (MQ=255)
                                                    tCCCGTTTCGTACTGTACATCTTCCATCCAGCGGGTATAc                                                 >  1:250096/1‑40 (MQ=255)
                                                      ccGTTTCGTATTGTATATCTTCCATCCAGCGGGTATACTGa                                              <  1:1145073/41‑1 (MQ=255)
                                                      ccGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCACACGTATCCAg                 <  1:442186/70‑1 (MQ=255)
                                                        gTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTa                                  >  1:3960734/1‑51 (MQ=255)
                                                         tttCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCccttcc                                      >  1:3188831/1‑46 (MQ=255)
                                                         tttCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCACACGTa                      >  1:1107257/1‑62 (MQ=255)
                                                         tttCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCACACGTATCCAGCAc              >  1:3359569/1‑70 (MQ=255)
                                                         tttCGTACTGTACATCTTCCATCCAGCGGGTATACTGATCccttcctt                                    <  1:4127498/48‑1 (MQ=255)
                                                           tCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCACACGTATCCAGCACGa            <  1:2107128/70‑1 (MQ=255)
                                                           tCGTACTGTACATCTTCCATCCAGCGGGTATACTGATCccttc                                       >  1:3305453/1‑43 (MQ=255)
                                                           tCGTACTGTACATCTTCCATCCAGCGGGTATACTGATCccttc                                       >  1:2966415/1‑43 (MQ=255)
                                                            cGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCACACGTATCCAGCACGa            <  1:650441/69‑1 (MQ=255)
                                                              tACTGTACATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCACACGTATCCAGCACGAaata        <  1:1820406/71‑1 (MQ=255)
                                                                    atatCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCca                            >  1:663954/1‑45 (MQ=255)
                                                                    atatCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCACACGTATCCAGCACGAAATAATATg   >  1:1878885/1‑70 (MQ=255)
                                                                     tatCTTCCATCCAGCGGGTATACTGATCCCTTCCttt                                   <  1:1048801/37‑1 (MQ=255)
                                                                     tatCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCACACGTATCCAGCACGGAATAatat    >  1:3023890/1‑68 (MQ=255)
                                                                     tatCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCACACGTATCCAGCACGAAATAatat    <  1:2439391/68‑1 (MQ=255)
                                                                     tatCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCACACGTATCCAGCACGAAATAATATGc  >  1:2803874/1‑70 (MQ=255)
                                                                     |                                                                     
TTGACGCGGATGGCCATTTTTTGCATCTTTCCATGCGTTAAGCCCTGCTTTTTCCCGTTTCGTACTGTATATCTTCCATCCAGCGGGTATACTGATCCCTTCCTTTAAATCCACACGTATCCAGCACGAAATAATATGC  >  W3110S.gb/3914964‑3915102

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