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
A20 F53 I6 R4 121 75.7 2723416 94.9% 2584521 126.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP006881 3,725,237 A→G intergenic (‑69/‑460) U712_19205 ← / → U712_19210 Uncharacterized protein ywcI/Minor extracellular protease vpr

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068813,725,2370AG76.7% 86.5 / 1.7 43intergenic (‑69/‑460)U712_19205/U712_19210Uncharacterized protein ywcI/Minor extracellular protease vpr
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (25/8);  minor base C (0/10);  total (25/18)
Fisher's exact test for biased strand distribution p-value = 2.28e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑C‑TTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTTTAG  >  CP006881/3725119‑3725363
                                                                                                                           |                                                                                                                              
ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAACCATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑C‑TTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAttt                                                                                                            >  5:94324/1‑139 (MQ=255)
     caAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAgttcttt                                                                                                        >  7:155857/1‑139 (MQ=255)
               aTCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTAGCaaa                                                                                               >  7:140267/1‑138 (MQ=255)
                          tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGctg                                                                                     >  5:157389/1‑136 (MQ=255)
                          tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCGTTTCTCGCAAACTAGCGGctc                                                                                     >  1:276090/1‑137 (MQ=255)
                          tAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCGTTTCTCGCAAACTAGCGGctc                                                                                     >  7:274320/1‑137 (MQ=255)
                          tAAAGATACAACCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTATGGCAGG‑CTG‑C‑CTTTTTA‑GCAGCCCGATATCTCCGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCGAACTAGCGGCTCTa                                                                                   >  6:234321/1‑139 (MQ=255)
                             acaTACAACAAAACGTTTAATATAAAAACATCCCTCCGTTTTTTTTGGGCCGT‑CTG‑CTT‑TTTTC‑GACGCCGTTTTTTTCCGCCCCCGCCCCAAATAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa                                                                                <  4:220454/137‑1 (MQ=255)
                             aGATACAAGCAAAGTTTTCATTGAAAAACTGCCCACCGCTTCTTTTGGCCTGG‑CAG‑C‑CTTTTTA‑GCTGCGGTTTTTCACAGCCGCCGCCCGCAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa                                                                                <  8:54389/139‑1 (MQ=255)
                              gaaaaaaGCACACGTTTAATACAAAAACAGCCCTCCGCTTCTTTTTGCCCGC‑CTG‑C‑CTTTTTC‑GCCGCCGTTTTTCTCCGCCCCACCCCCCAAGAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCaa                                                                               <  6:117983/134‑1 (MQ=255)
                                 aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTGGCAAACTAGCGTCTCTAGCAAAAc                                                                            >  5:54903/1‑139 (MQ=255)
                                 aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCGCAAACTAGCGGGGCTAGCaaaa                                                                             >  2:290331/1‑138 (MQ=255)
                                 aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAACAAAAGACGGCCGATTTCTTTTCTCGCAAACTATCGGCTCAAGCaaaa                                                                             >  3:220454/1‑138 (MQ=255)
                                 aCAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGGTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCATTTCTCGCAAACTAGCGGCGCTAGCaaaa                                                                             >  5:318709/1‑138 (MQ=255)
                                    aGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCCGCCGCAGCCCCAAATAAAACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCa                                                                         <  4:284000/139‑1 (MQ=255)
                                     gCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCACCCCGCATGAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                        <  7:59620/139‑1 (MQ=255)
                                     ccAAACGTTTAATATAAAAACATCCCTCCGCTTATTTTTGGCCGG‑AAGAC‑T‑TTTTC‑GCAGCCCGTTTTCTACGCCGCAGCCCCAAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                        <  6:157389/138‑1 (MQ=255)
                                       aaaGGTTTAATACAAAAACAGCCCCCCGCTTCTTTTGGGCCGG‑CCC‑C‑CTTTTTA‑CCCCCCGGTTTTCTCCGCCCCCCCCCGAAACAACCCACGGCCGATTTCTTTTCTCGCAAACTCGCGGCTCTAGCAAAACTCATGa                                                                      <  1:316627/139‑1 (MQ=255)
                                       aaaCGTTTCATCTAAAAACAACCCTCGGTTTCTTTTTGGCCGC‑CTG‑CTT‑TTTTA‑GCCGCCCGTTTTCTCTGCCGCTGCCCGCAAGAATCGACGGCCGTTTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa                                                                      <  4:153597/139‑1 (MQ=255)
                                       aaaCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCCGCCCCCAATAAAACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa                                                                      <  7:206937/139‑1 (MQ=255)
                                       aaaCGTTTAATATAAAAACATCCCACCGATGCTTTTTGGCCGC‑CAG‑C‑CTTTTTA‑GCACCCCGTTTGCTCCGCCCCCCCCCCCAACAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa                                                                      <  3:157817/139‑1 (MQ=255)
                                       aaaCGTTCAATATAAAAACAACCCTCCGATTTTTTTGGGCTGC‑CAG‑CAT‑TTTTC‑CCAGCCGGTTTACACCGCCGCCGCCCGAAATAAAACACGGCCTATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGa                                                                      <  5:291930/139‑1 (MQ=255)
                                         ccGTTTAAAAAAAAAACATCCCTCCGTTTCTTTTGGGCTGC‑CCG‑CAT‑TTTTA‑GACGCCGTTTTTACCACCCGCCGCCCCAAACAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                    <  6:195497/138‑1 (MQ=255)
                                         ccGTTACAAACAAAAACATCCCCCGGGTGCTTTTGGGCGGG‑CAG‑CGT‑TTTTC‑GCCGCCCGTTTGCCCCGCCGCCCCCCCAAAAAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                    <  1:226990/138‑1 (MQ=255)
                                         acttttCATACAAAACCACCCCGCCGCTTATTTTGGCCCGG‑CCG‑C‑CTTTTTC‑GCCGCCGGTTTCCCCCGCCGCCCCCCGCAAAAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                    <  1:42571/136‑1 (MQ=255)
                                         aCGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGATTTCTTTTCTCGCAAACTAGCGGCGCGAGCCAAACTCATGAc                                                                     >  7:123259/1‑138 (MQ=255)
                                         aCGTTTCATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGATTTCTTTTCTCGCAAACTAGCCGCGCAAGCAAAACACATgcc                                                                     >  5:177339/1‑136 (MQ=255)
                                         aCGTTTCATACAAAAACATCCCTCCGATTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCCGCCCCAGCCCGAACTAAACGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                    <  8:257323/139‑1 (MQ=255)
                                              caatccaaaacCATCCGCCCGATTATTTTTGCCAGC‑CCT‑C‑T‑TTTTACGCAGCCCTTTTGCTCCGCCGACCCCCCCAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATg                                                               <  4:290724/133‑1 (MQ=255)
                                               cATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CCG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTGTTTTATCGCAAACTAGCCGCGCTAGCAAAACTCATGACGCTATGa                                                              >  4:122532/1‑139 (MQ=255)
                                                atatAAAAAAATCCGTCCGTTTTTTTTTGGATGGACGA‑T‑T‑TTTTA‑GCCCCCGTTTTTCTCACCCCCAGCCCCAAAAAAACCAGGGCCGATTTCTTTTCTCTCAAAGTAGCGGCTATAGCAAAACTCATGACTCTATGAt                                                             <  8:140267/139‑1 (MQ=255)
                                                     aaaaCATCCCTCCGCTTATTTTTGGCCGG‑CAG‑C‑CGTTTTA‑GCATCCCGTTTTCTCAGCCCCACCCCGCAACAAAAGCCCGCCGATTTCTTATCGCCCAAACTAGCGGCGCTACCAAAAACCATCACACCATTATAGAcc                                                        >  4:183984/1‑139 (MQ=255)
                                                      aaaCATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑CTTTTTA‑GCACCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAATTCAAGTCTCGCAAACTACCGGCTCTAGCAAAACTCATGACTCTATGATAGACCg                                                       >  5:130828/1‑139 (MQ=255)
                                                                                               a‑gcagcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGaaaaaa                 >  6:294405/1‑139 (MQ=255)
                                                                                                   agcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTGTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTTGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAAcc               >  2:89381/1‑138 (MQ=255)
                                                                                                   agcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGTAAGAGAATTCTTTGTCACAAAAAGAGTGAAAAAAcc               >  3:131201/1‑138 (MQ=255)
                                                                                                    gcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTGATTTATCGCAAACTTGCGGCTGGAGCAAATCTCATGGCTCTATGATAGCCCCGGGAAAGAGATTTCTTTGGGGGCATTTGAGTGaaaaaagcta             >  4:63901/1‑135 (MQ=255)
                                                                                                    gcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCa                                                                                                 >  7:29698/1‑55 (MQ=255)
                                                                                                    gcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCa                                                                                                 <  8:29698/55‑1 (MQ=255)
                                                                                                    gcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACGCATGTATCGATGATAGTCCGTGGTAAGAGAATTCTATGTCACAATATGTGTGAAAAAACCaa             >  8:166851/1‑139 (MQ=255)
                                                                                                     cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAATAGAATTCTTTTTCACAATATGATTTAAAAAACCaa             >  1:147010/1‑138 (MQ=255)
                                                                                                               cAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGtttt     >  3:225632/1‑136 (MQ=255)
                                                                                                                aGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAAATAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGTAAAGAGAATTCTTTGTCTAAATATGAGTGAAAAAACAAACTAGTTTTTAg  >  6:99217/1‑138 (MQ=255)
                                                                                                                           |                                                                                                                              
TTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTTCATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGG‑CAG‑C‑C‑TTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTTTAG  >  CP006881/3725119‑3725363

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A