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 3,018,853 C→T 12.0% T346I (ACT→ATT)  ssnA → predicted chlorohydrolase/aminohydrolase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,018,8530CT12.0% 218.1 / 16.8 75T346I (ACT→ATT) ssnApredicted chlorohydrolase/aminohydrolase
Reads supporting (aligned to +/- strand):  ref base C (27/39);  new base T (5/4);  total (32/43)
Fisher's exact test for biased strand distribution p-value = 4.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

AATTTGCCTTCTTTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCTGGAAGCCGGTTACAAAGC  >  W3110S.gb/3018784‑3018922
                                                                     |                                                                     
aaTTTGCCTTCTTTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGAc                                                                       >  1:988208/1‑70 (MQ=255)
aaTTTGCCTTCTTTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGAc                                                                       >  1:326983/1‑70 (MQ=255)
  tttGCCTTCTTTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTaa                                                                    <  1:1720363/71‑1 (MQ=255)
  tttGCCTTCTTTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTa                                                                     <  1:3361574/70‑1 (MQ=255)
   ttGCCTTCTTTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAAc                                                                   >  1:2388245/1‑71 (MQ=255)
    tGCCTTCTTTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACg                                                                  >  1:1960494/1‑71 (MQ=255)
      ccTTCTTTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACt                                                                      <  1:1563754/65‑1 (MQ=255)
       cttcttTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTa                                                               <  1:1954775/71‑1 (MQ=255)
          cttTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGATTAACGGTAAc                                                             >  1:3094648/1‑70 (MQ=255)
          cttTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAAc                                                             >  1:1202122/1‑70 (MQ=255)
          cttTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAAc                                                             >  1:3041716/1‑70 (MQ=255)
          cttTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAAc                                                             >  1:4568361/1‑70 (MQ=255)
           tttAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGATTAACGGTAACg                                                            >  1:1273635/1‑70 (MQ=255)
             tAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGATTAACGGTAACGAAc                                                         >  1:2797116/1‑71 (MQ=255)
             tAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGATTAACGGTAACGAAc                                                         >  1:3905561/1‑71 (MQ=255)
             tAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACg                                                            <  1:3207183/68‑1 (MQ=255)
                aCATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAAc                                                             <  1:3081255/64‑1 (MQ=255)
                  aTCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACtgatg                                                    <  1:518658/71‑1 (MQ=255)
                  aTCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACtgatg                                                    <  1:3035840/71‑1 (MQ=255)
                       gATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCg                                               >  1:1558145/1‑71 (MQ=255)
                         tGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTaa                                                                    <  1:3142445/48‑1 (MQ=255)
                            gggTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGATTAACGGTAACGAACTGATGAGCCGCAACt                                          <  1:4293802/71‑1 (MQ=255)
                            gggTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACt                                          <  1:3004291/71‑1 (MQ=255)
                             ggtggtCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACtt                                         <  1:3417699/71‑1 (MQ=255)
                             ggtggtCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACtt                                         <  1:3879978/71‑1 (MQ=255)
                               tggtCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACttt                                        <  1:3827278/70‑1 (MQ=255)
                               tggtCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTg                                       <  1:4408814/71‑1 (MQ=255)
                               tggtCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTg                                       <  1:1145689/71‑1 (MQ=255)
                               tggtCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTg                                       <  1:1064038/71‑1 (MQ=255)
                               tggtCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTg                                       <  1:1246175/71‑1 (MQ=255)
                                 gtCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCa                                             <  1:4295700/63‑1 (MQ=255)
                                  tCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAg                                                  <  1:2209181/57‑1 (MQ=255)
                                  tCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTg                                       <  1:4164708/68‑1 (MQ=255)
                                   ccGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCa                                             <  1:2627337/61‑1 (MQ=255)
                                   ccGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGtcgc                                   >  1:4384123/1‑71 (MQ=255)
                                    cGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGc                                              >  1:515774/1‑59 (MQ=255)
                                     gCTGTGGCCTGACAGTTTTGCCAAAGCCCTGATTAACGGTAACGAACTGATGAGCCGCAACttt                                        >  1:1732185/1‑64 (MQ=255)
                                      cTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACg                                                            <  1:737493/43‑1 (MQ=255)
                                        gtgGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAg                                                  <  1:697496/51‑1 (MQ=255)
                                        gtgGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGcc                                                >  1:2590561/1‑53 (MQ=255)
                                         tgGCCTGACAGTTTTGCCAAAGCCCTGATTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGaaa                               <  1:701557/69‑1 (MQ=255)
                                         tgGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACtgatg                                                    >  1:545550/1‑48 (MQ=255)
                                         tgGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAAtt                             >  1:2073177/1‑71 (MQ=255)
                                           gCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTgg                                      >  1:4115481/1‑60 (MQ=255)
                                           gCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTg                                       >  1:1948053/1‑59 (MQ=255)
                                           gCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGgc                                     >  1:2575966/1‑61 (MQ=255)
                                           gCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGgc                                     >  1:3440750/1‑61 (MQ=255)
                                           gCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAAttt                            <  1:3072002/70‑1 (MQ=255)
                                           gCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAAttt                            <  1:3317542/70‑1 (MQ=255)
                                            ccTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAAtt                             <  1:3599136/68‑1 (MQ=255)
                                             cTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACg                                                            <  1:714094/36‑1 (MQ=255)
                                             cTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAAc                                                         <  1:1669045/39‑1 (MQ=255)
                                               gACAGTTTTGCCAAAGCCCTGACTAACGGTAACGaa                                                          >  1:2408982/1‑36 (MQ=255)
                                                aCAGTTTTGCCAAAGCCCTGATTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCtt                      <  1:1750681/71‑1 (MQ=255)
                                                aCAGTTTTGCCAAAGCCCTGACTAACGGTAACGaa                                                          >  1:2544153/1‑35 (MQ=255)
                                                aCAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGc                                                 >  1:728118/1‑44 (MQ=255)
                                                aCAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACttt                                        <  1:1836442/53‑1 (MQ=255)
                                                   gTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCTg                   <  1:1744559/71‑1 (MQ=255)
                                                    ttttGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGcgcg                                  <  1:1924955/55‑1 (MQ=255)
                                                    ttttGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCt                       <  1:4076770/66‑1 (MQ=255)
                                                    ttttGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCTgg                  <  1:2907473/71‑1 (MQ=255)
                                                       tGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCTGGaa                <  1:924055/70‑1 (MQ=255)
                                                        gCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCTGGAAGc              >  1:3113670/1‑71 (MQ=255)
                                                         ccAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAAtt                             <  1:2588170/55‑1 (MQ=255)
                                                          cAAAGCCCTGATTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAAtt                             <  1:3823882/54‑1 (MQ=255)
                                                            aaGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTg                           <  1:4162267/54‑1 (MQ=255)
                                                            aaGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCTGGAAGCCGGt          >  1:2556206/1‑71 (MQ=255)
                                                            aaGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCTGGAAGCCGGt          >  1:1461047/1‑71 (MQ=255)
                                                             aGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCTGGAAGCCGGt          >  1:20850/1‑70 (MQ=255)
                                                             aGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCTGGAAGCCGGt          >  1:4530740/1‑70 (MQ=255)
                                                             aGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCTGGAAGCCGGt          >  1:754618/1‑70 (MQ=255)
                                                               cccTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAAtt                             <  1:3793393/49‑1 (MQ=255)
                                                               cccTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCt                    <  1:4358823/58‑1 (MQ=255)
                                                                ccTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTgg                          <  1:135320/51‑1 (MQ=255)
                                                                 cTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGgc                                     >  1:710522/1‑39 (MQ=255)
                                                                 cTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGgc                                     >  1:854666/1‑39 (MQ=255)
                                                                    aCTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCTGGAAGCCGGTTACAAAGc  >  1:3679029/1‑71 (MQ=255)
                                                                     |                                                                     
AATTTGCCTTCTTTAAACATCGCGATGCGGGTGGTCCGCTGTGGCCTGACAGTTTTGCCAAAGCCCTGACTAACGGTAACGAACTGATGAGCCGCAACTTTGGCGCGAAATTTGGGCTTCTGGAAGCCGGTTACAAAGC  >  W3110S.gb/3018784‑3018922

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