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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,872,394 C→T 21.5% S339S (AGC→AGT)  ygcE → predicted kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,872,3940CT21.5% 185.1 / 38.1 129S339S (AGC→AGT) ygcEpredicted kinase
Reads supporting (aligned to +/- strand):  ref base C (43/58);  new base T (13/15);  total (56/73)
Fisher's exact test for biased strand distribution p-value = 8.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.83e-01

Only 100 of 129 total aligned reads displayed.

CTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTGAAGAACAATT  >  minE/1872334‑1872458
                                                            |                                                                
cTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTa                                                          >  1:3036294/1‑69 (MQ=255)
cTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTa                                                          >  1:1619568/1‑69 (MQ=255)
cTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTa                                                          >  1:199591/1‑69 (MQ=255)
cTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTa                                                          >  1:1473098/1‑69 (MQ=255)
cTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTa                                                          >  1:1437636/1‑69 (MQ=255)
cTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTa                                                          >  1:2437249/1‑69 (MQ=255)
cTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTa                                                          >  1:528360/1‑69 (MQ=255)
cTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTa                                                          >  1:542794/1‑69 (MQ=255)
cTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTa                                                          >  1:1178477/1‑69 (MQ=255)
cTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTa                                                          >  1:86952/1‑69 (MQ=255)
cTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTa                                                          >  1:893203/1‑69 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:3426029/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:3161343/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:3070727/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:960788/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:2726170/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:2415320/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:2366582/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:711200/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:2214540/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:1789187/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:1290215/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:1616645/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:1188606/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:111225/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:1598254/69‑1 (MQ=255)
  ggCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:1123614/69‑1 (MQ=255)
   gCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGAt                                                            <  1:2768556/64‑1 (MQ=255)
   gCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGAt                                                            <  1:1428332/64‑1 (MQ=255)
   gCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGAt                                                            <  1:3167692/64‑1 (MQ=255)
    cTGTCCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACg                                                        <  1:2388127/67‑1 (MQ=255)
      gACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATg                                                    <  1:2782835/69‑1 (MQ=255)
      gACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATg                                                    <  1:2218495/69‑1 (MQ=255)
      gACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATg                                                    <  1:3334605/69‑1 (MQ=255)
      gACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATg                                                    <  1:213322/69‑1 (MQ=255)
      gACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATg                                                    <  1:2396024/69‑1 (MQ=255)
      gACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATg                                                    <  1:847770/69‑1 (MQ=255)
      gACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATg                                                    <  1:288095/69‑1 (MQ=255)
          aaTCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGata                                                <  1:1294686/69‑1 (MQ=255)
          aaTCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGata                                                <  1:290325/69‑1 (MQ=255)
          aaTCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGata                                                <  1:141353/69‑1 (MQ=255)
          aaTCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGata                                                <  1:495859/69‑1 (MQ=255)
          aaTCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGata                                                <  1:2117271/69‑1 (MQ=255)
          aaTCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGata                                                <  1:741898/69‑1 (MQ=255)
          aaTCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGata                                                <  1:1960199/69‑1 (MQ=255)
          aaTCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGata                                                <  1:1867158/69‑1 (MQ=255)
          aaTCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGata                                                <  1:1878459/69‑1 (MQ=255)
            tCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGata                                                <  1:2010667/67‑1 (MQ=255)
                tGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGATATATCGt                                          <  1:298852/69‑1 (MQ=255)
                 gggAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGAt                                                            <  1:1322083/50‑1 (MQ=255)
                  ggAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGata                                                >  1:1071395/1‑61 (MQ=255)
                  ggAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGATATATCGTTc                                        <  1:2521996/69‑1 (MQ=255)
                       cGTACAAACGCGGGATTATGATCGGCTTTGAATCCAGCATGGATTACGCATGGata                                                <  1:1899284/56‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcg                     <  1:3096747/69‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcg                     <  1:1015106/69‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcg                     <  1:932660/69‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcg                     <  1:1651910/69‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcg                     <  1:3120127/69‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcg                     <  1:1207996/69‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcg                     <  1:3344395/69‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcg                     <  1:1700401/69‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcg                     <  1:2678878/69‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcg                     <  1:2472776/69‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcg                     <  1:2437144/69‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcg                     <  1:1461464/69‑1 (MQ=255)
                                     aTTATGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTGCGATACTGGAAAGCGTGgcg                     <  1:749540/69‑1 (MQ=255)
                                        aTGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcaga                   >  1:1646638/1‑65 (MQ=255)
                                        aTGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcaga                   >  1:2825762/1‑65 (MQ=255)
                                        aTGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgcaga                   >  1:2140789/1‑65 (MQ=255)
                                        aTGATCGGCTTTGATTCCAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGgca                     >  1:2074435/1‑65 (MQ=255)
                                           aTCGGCTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGcgctgacg               >  1:2805966/1‑69 (MQ=255)
                                           aTCGGCTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGcgctgacg               >  1:940384/1‑69 (MQ=255)
                                           aTCGGCTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGcgctgacg               >  1:1911377/1‑69 (MQ=255)
                                           aTCGGCTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGcgctgacg               >  1:701003/1‑69 (MQ=255)
                                           aTCGGCTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGcgctgacg               >  1:367959/1‑69 (MQ=255)
                                           aTCGGCTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGcgctgacg               >  1:3392867/1‑69 (MQ=255)
                                           aTCGGCTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGcgctgacg               >  1:2997804/1‑69 (MQ=255)
                                           aTCGGCTTTGATTCCAGCATGGATTAAGCATGGATATATCGTTCGATACTGGAAAGCGTGGcgctgacg               >  1:153233/1‑69 (MQ=255)
                                              ggCTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGcgctgacgctg            <  1:3199986/69‑1 (MQ=255)
                                                cTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGcgctgacgctga           >  1:2782971/1‑68 (MQ=255)
                                                cTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGcgctgacgctga           >  1:2548023/1‑68 (MQ=255)
                                                cTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGcgctgacgctga           >  1:3232675/1‑68 (MQ=255)
                                                atttGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTgg                       >  1:285211/2‑56 (MQ=255)
                                                 tttGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTgaag         <  1:396748/69‑1 (MQ=255)
                                                 tttGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTgaag         <  1:1325027/69‑1 (MQ=255)
                                                  ttGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTgaaga        <  1:2405846/69‑1 (MQ=255)
                                                   tGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTTGCGCTGACGCTgaaga        >  1:1654065/1‑68 (MQ=255)
                                                   tGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTgaaga        >  1:2340672/1‑68 (MQ=255)
                                                   tGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTgaaga        >  1:2025015/1‑68 (MQ=255)
                                                   tGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTgaaga        >  1:3198143/1‑68 (MQ=255)
                                                   tGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTgaaga        >  1:1930650/1‑68 (MQ=255)
                                                     aTTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTGAAGAAc      <  1:2216351/68‑1 (MQ=255)
                                                     aTTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTGAAGAAc      <  1:2999699/68‑1 (MQ=255)
                                                      ttCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTGAAGAACa     <  1:2299848/68‑1 (MQ=255)
                                                      ttCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTGAAGAACa     <  1:2733975/68‑1 (MQ=255)
                                                         cAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTGAAGaataat   >  1:1461656/1‑67 (MQ=255)
                                                         cAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTGAAGAATAAtt  >  1:3031088/1‑68 (MQ=255)
                                                         cAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTGAAGAATAAtt  >  1:2655227/1‑68 (MQ=255)
                                                         cAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTGAAGAATAAtt  >  1:445677/1‑68 (MQ=255)
                                                         cAGTATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTGAAGAATAAtt  >  1:309722/1‑68 (MQ=255)
                                                            |                                                                
CTGGCTGACCAATCCGTGGGAACCGTACAAACGCGGGATTATGATCGGCTTTGATTCCAGCATGGATTACGCATGGATATATCGTTCGATACTGGAAAGCGTGGCGCTGACGCTGAAGAACAATT  >  minE/1872334‑1872458

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