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 3,704,876 C→T 8.2% M164I (ATG→ATA)  trkD ← potassium transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,704,8760CT 8.2% 187.6 / 6.0 61M164I (ATG→ATA) trkDpotassium transporter
Reads supporting (aligned to +/- strand):  ref base C (31/24);  new base T (2/3);  total (33/28)
Fisher's exact test for biased strand distribution p-value = 6.49e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.97e-01

CGTAACCCCAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTGAGAGGGGAACTATCCAG  >  W3110S.gb/3704811‑3704945
                                                                 |                                                                     
cGTAACCCCAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGc                                                                  >  1:758906/1‑71 (MQ=255)
 gTAACCCCAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGcc                                                                 >  1:4298077/1‑71 (MQ=255)
   aaCCCCAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCa                                                                      >  1:956468/1‑64 (MQ=255)
    aCCCCAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTg                                                              >  1:1269624/1‑71 (MQ=255)
     ccccAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGc                                                             <  1:1539361/71‑1 (MQ=255)
     ccccAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGc                                                             >  1:1715639/1‑71 (MQ=255)
      cccAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACTATAGCCGTGc                                                             >  1:4077933/1‑70 (MQ=255)
      cccAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCAt                                                                     <  1:549755/62‑1 (MQ=255)
      cccAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGcc                                                            <  1:501002/71‑1 (MQ=255)
       ccAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCa                                                           >  1:1248491/1‑71 (MQ=255)
        cAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCa                                                                      >  1:369523/1‑59 (MQ=255)
         aGTCCTGGCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATg                                                         >  1:1617717/1‑71 (MQ=255)
         aGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATg                                                         >  1:4531762/1‑71 (MQ=255)
          gTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGt                                                        <  1:705061/71‑1 (MQ=255)
           tCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGc                                                                  <  1:2111264/60‑1 (MQ=255)
             cTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGtttt                                                     >  1:1431884/1‑71 (MQ=255)
             cTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGtttt                                                     >  1:2984645/1‑71 (MQ=255)
             cTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGttt                                                      <  1:3707284/70‑1 (MQ=255)
             cTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGttt                                                      <  1:3862853/70‑1 (MQ=255)
               gCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGttttt                                                    >  1:407310/1‑70 (MQ=255)
                 cAGTATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGaa                                                 <  1:2598187/71‑1 (MQ=255)
                 cAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGaa                                                 >  1:1425902/1‑71 (MQ=255)
                   gAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAAt                                                >  1:4130961/1‑70 (MQ=255)
                     aTCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACTATAGcc                                                                 >  1:3041539/1‑51 (MQ=255)
                        aaaaaCCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTg                                                   >  1:3951291/1‑62 (MQ=255)
                        aaaaaCCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTg                                                   >  1:697672/1‑62 (MQ=255)
                          aaaCCAGGTCAGCATGATTGGCGCAAACAGCTTACCGAcc                                                                       >  1:3553484/1‑40 (MQ=255)
                           aaCCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCa                                              <  1:1847125/64‑1 (MQ=255)
                              cAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAataata                                     >  1:1023219/1‑70 (MQ=255)
                               aGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATaaa                                   <  1:4213770/71‑1 (MQ=255)
                                ggTCAGCATGATCGGCGCAAACAGCTTACCGAACATAGcc                                                                 >  1:2934886/1‑40 (MQ=255)
                                   cAGCATGATCGGCGCAAACAGCTTACCGACCATAGc                                                                  >  1:926279/1‑36 (MQ=255)
                                     gCATGATCGGCGCAAACAGCTTACCGACAATAGCCGTGCCATGTTTTTGAATCata                                            <  1:190219/56‑1 (MQ=255)
                                       aTGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGttttt                                                    >  1:4091113/1‑46 (MQ=255)
                                        tGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGttt                                                      <  1:441068/43‑1 (MQ=255)
                                          aTCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAataata                                     >  1:3241155/1‑58 (MQ=255)
                                          aTCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGa                         <  1:373022/70‑1 (MQ=255)
                                          aTCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGa                         >  1:2774986/1‑70 (MQ=255)
                                          aTCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGAt                        <  1:2897195/71‑1 (MQ=255)
                                          aTCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGAt                        <  1:2084813/71‑1 (MQ=255)
                                           tCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGt                                 >  1:202841/1‑61 (MQ=255)
                                           tCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGa                         >  1:3444053/1‑69 (MQ=255)
                                           tCGGCACAAACAGCTTACCGACCATAGCCGTGCCAt                                                          >  1:2731470/1‑36 (MQ=255)
                                            cGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCat                                             >  1:462273/1‑48 (MQ=255)
                                             ggCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATaa                      <  1:2260386/70‑1 (MQ=255)
                                               cgcAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTg                   <  1:425260/71‑1 (MQ=255)
                                                 cAAACAGCTTACCGACTATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTgag                              <  1:3651111/58‑1 (MQ=255)
                                                 cAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTgag                 <  1:2752242/71‑1 (MQ=255)
                                                  aaaCAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAAtt                    <  1:3697572/67‑1 (MQ=255)
                                                  aaaCAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAAtt                    <  1:4283301/67‑1 (MQ=255)
                                                  aaaCAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTga                  >  1:772914/1‑69 (MQ=255)
                                                   aaCAGCTTACCGACTATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTgag                 <  1:4557673/69‑1 (MQ=255)
                                                    aCAGCTTACCGCCCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTGAGAgg              >  1:1852334/1‑71 (MQ=255)
                                                     cAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATc                                               <  1:96894/37‑1 (MQ=255)
                                                     cAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTGAGAgg              <  1:4333550/70‑1 (MQ=255)
                                                      aGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCaaaaat                                         >  1:453324/1‑42 (MQ=255)
                                                       gCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTga                  <  1:994714/64‑1 (MQ=255)
                                                       gCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTGAGAgggg            >  1:4345856/1‑70 (MQ=255)
                                                        cTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTGAGAGGGGaa          >  1:3312093/1‑71 (MQ=255)
                                                           aCCGACTATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGt                                 <  1:3503466/45‑1 (MQ=255)
                                                              gACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTGAGAGGGGAACTATcc    <  1:3953550/71‑1 (MQ=255)
                                                              gACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTGAGAGGGGAACTATcc    <  1:3871387/71‑1 (MQ=255)
                                                                ccATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTGAGAGGGGAACTATCCAg  >  1:1562608/1‑71 (MQ=255)
                                                                 |                                                                     
CGTAACCCCAGTCCTGCCAGAATCAAAAACCAGGTCAGCATGATCGGCGCAAACAGCTTACCGACCATAGCCGTGCCATGTTTTTGAATCATAAATAATAAAGTGAGAACGATAATTGAGAGGGGAACTATCCAG  >  W3110S.gb/3704811‑3704945

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A