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
A12 F133 I1 R1 102 83.9 4092546 96.1% 3932936 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,594,073 G→T T45N (ACC→AAC)  livG ← branched‑chain amino acid ABC transporter ATPase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,594,0730GT95.2% 209.7 / 2.0 62T45N (ACC→AAC) livGbranched‑chain amino acid ABC transporter ATPase
Reads supporting (aligned to +/- strand):  ref base G (2/1);  new base T (28/31);  total (30/32)
Fisher's exact test for biased strand distribution p-value = 6.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

TTTGCTGCCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGGTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGGCCGCCGAAGCGCATC  >  NC_000913/3593978‑3594171
                                                                                               |                                                                                                  
tttGCTGCCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTtttt                                                                                                >  1:2038839/1‑100 (MQ=255)
 ttGCTGCCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGtttttt                                                                                               <  2:1690057/100‑1 (MQ=255)
  tgctgcCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTc                                                                                              >  2:573701/1‑100 (MQ=255)
   gctgcCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTcc                                                                                             <  2:1474262/100‑1 (MQ=255)
    ctgcCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCg                                                                                            <  1:1155329/100‑1 (MQ=255)
    ctgcCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCg                                                                                            >  1:1224720/1‑100 (MQ=255)
      gcCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGc                                                                                          >  2:122356/1‑100 (MQ=255)
        cccGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCAc                                                                                        <  1:1566203/100‑1 (MQ=255)
          cGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCg                                                                                      <  1:1916322/100‑1 (MQ=255)
           ggTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGt                                                                                     <  2:664365/100‑1 (MQ=255)
                 ccTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGc                                                                               >  2:921924/1‑100 (MQ=255)
                 ccTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGc                                                                               >  1:1716691/1‑100 (MQ=255)
                  cTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGcc                                                                              >  2:1688446/1‑100 (MQ=255)
                   ttCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCg                                                                             <  2:1450386/100‑1 (MQ=255)
                     ccAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAACACCGTGTTTTTTCCGGCACCGTTAGGGCCGAt                                                                           <  2:1322360/100‑1 (MQ=255)
                           gCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACga                                                                     <  2:477501/100‑1 (MQ=255)
                           gCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACga                                                                     >  2:1034404/1‑100 (MQ=255)
                           gCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACga                                                                     >  1:585358/1‑100 (MQ=255)
                            cTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGGTTTTTCCGGCACCGTTAGGGCCGATTAACgag                                                                    <  2:442712/100‑1 (MQ=255)
                             tGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACgaga                                                                   <  2:237205/100‑1 (MQ=255)
                              gATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGAc                                                                  >  1:1473447/1‑100 (MQ=255)
                                  gcgcAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGAtc                                                              <  1:1354856/100‑1 (MQ=255)
                                  gcgcAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGAtc                                                              >  1:1268832/1‑100 (MQ=255)
                                  gcgcAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGAtc                                                              <  2:139594/100‑1 (MQ=255)
                                    gcAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGAtctc                                                            >  1:988821/1‑100 (MQ=255)
                                     cAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTcc                                                           <  2:23560/100‑1 (MQ=255)
                                      aGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCt                                                          <  2:1288724/100‑1 (MQ=255)
                                       gTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTg                                                         >  1:402471/1‑100 (MQ=255)
                                       gTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGGTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTg                                                         >  2:742872/1‑100 (MQ=255)
                                         aaaaTGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCg                                                       <  2:1537350/100‑1 (MQ=255)
                                         aaaaTGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCg                                                       <  2:214721/100‑1 (MQ=255)
                                          aaaTGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCgg                                                      <  1:1688459/100‑1 (MQ=255)
                                          aaaTGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCg                                                       >  2:356038/1‑99 (MQ=255)
                                           aaTGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCggg                                                     <  1:1051090/100‑1 (MQ=255)
                                            aTGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGt                                                    >  2:1917616/1‑100 (MQ=255)
                                                    gccgGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGGCGATCTCCTGCGGGTACAGTTCa                                            >  1:353669/1‑100 (MQ=255)
                                                      cgGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAg                                          <  1:573703/100‑1 (MQ=255)
                                                      cgGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAg                                          <  2:922047/100‑1 (MQ=255)
                                                         tGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGAtt                                       >  1:197373/1‑100 (MQ=255)
                                                          gggTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTg                                      <  2:500375/100‑1 (MQ=255)
                                                           ggTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGa                                     >  1:1572218/1‑100 (MQ=255)
                                                           ggTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGa                                     <  2:1224714/100‑1 (MQ=255)
                                                             tttGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACg                                   <  2:225021/100‑1 (MQ=255)
                                                              ttGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTTTTTTTTTTTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACgt                                  >  2:712052/1‑100 (MQ=255)
                                                              ttGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACgt                                  <  1:607187/100‑1 (MQ=255)
                                                               tGTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACgtt                                 >  2:157194/1‑100 (MQ=255)
                                                               ngTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACgtt                                 >  1:732886/2‑100 (MQ=255)
                                                                gTAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACgttg                                >  1:2003511/1‑100 (MQ=255)
                                                                 tAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACgttgt                               <  2:1849051/100‑1 (MQ=255)
                                                                 tAGAATCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACgttgt                               <  1:475441/100‑1 (MQ=255)
                                                                      tCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCAcc                          >  2:681057/1‑100 (MQ=255)
                                                                      tCCGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCAcc                          <  2:1063161/100‑1 (MQ=255)
                                                                        cGGTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGc                        <  1:1917634/100‑1 (MQ=255)
                                                                          gTCAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCca                      <  2:147305/100‑1 (MQ=255)
                                                                            cAGACAGTTAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCcagc                    <  2:1572208/100‑1 (MQ=255)
                                                                                  gTTAAAAACCGTGGTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGgccg              >  2:1105368/1‑100 (MQ=255)
                                                                                   ttAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGgccgc             >  2:229558/1‑100 (MQ=255)
                                                                                   ttAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGgccgc             >  1:617240/1‑100 (MQ=255)
                                                                                    tAAAAACCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGgccgcc            >  2:517770/1‑100 (MQ=255)
                                                                                     aaaaaCCGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTGCACCGCCAGCAGGccgccg           >  2:920791/1‑100 (MQ=255)
                                                                                          ccGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGGCCGCCGAAgcg      <  1:1134299/100‑1 (MQ=255)
                                                                                          ccGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGGCCGCCGAAgcg      >  2:1271775/1‑100 (MQ=255)
                                                                                           cGTGTTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGGCCGCCGAAgcgc     <  2:1473438/100‑1 (MQ=255)
                                                                                            gtgtTTTTTCCGGCACCGTTAGTGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGGCCGCCGAAGCGca    <  2:935554/100‑1 (MQ=255)
                                                                                              ggTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGGCCGCCGAAGCGcatc  >  2:258165/1‑100 (MQ=255)
                                                                                               |                                                                                                  
TTTGCTGCCCCGGTAAACCTTCCAGGTGCTGATCGCGCAGTAAAATGGTGCCGCCGGTGGGTTTGTAGAATCCGGTCAGACAGTTAAAAACCGTGGTTTTTCCGGCACCGTTAGGGCCGATTAACGAGACGATCTCCTGCGGGTACAGTTCAAGATTGACGTTGTTCACCGCCAGCAGGCCGCCGAAGCGCATC  >  NC_000913/3593978‑3594171

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A