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
A26 F57 I1 R1 119 93.8 3687158 95.5% 3521235 127.0

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
*CP0068813,725,2370AG88.1% 91.6 / ‑3.0 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 (30/7);  minor base C (0/5);  total (30/13)
Fisher's exact test for biased strand distribution p-value = 9.31e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑C‑TTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTT  >  CP006881/3725114‑3725360
                                                                                                                                |                                                                                                                           
cccAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GGAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGc                                                                                                               >  5:192803/1‑139 (MQ=255)
cccAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGc                                                                                                               >  5:199749/1‑139 (MQ=255)
    gTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CATTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAt                                                                                                           >  1:299404/1‑139 (MQ=255)
     ttCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAtt                                                                                                          >  8:19855/1‑139 (MQ=255)
          caAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCCGCCCGCAAGAAAAGCCGGCCGAgttctgt                                                                                                     >  4:26443/1‑137 (MQ=255)
          caAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAgttcttt                                                                                                     >  1:405840/1‑139 (MQ=255)
          caAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCGTCTTTTTGGCAGGCAG‑C‑CGTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAgttattt                                                                                                     >  1:383664/1‑139 (MQ=255)
                    aTCCACACCCGTAAAGATACAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAAc                                                                                           >  4:422918/1‑139 (MQ=255)
                           cccGTCAAGAAACACCCAACCTTTT‑CATACAAAAACATCCCTCGGCTTGTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTACTCAGCCGCAGCCCTCAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGc                                                                                    <  7:39020/139‑1 (MQ=255)
                           cccGAAAACAAAAAACCAAACGTTC‑CAAACAAAAACATCCCGCGGCTTCTTTTTGGCCGCCAG‑C‑A‑TTTTACGCCCCCCTTTTTCTCAGCCGCCCCCCGAAACAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGc                                                                                    <  7:402937/139‑1 (MQ=255)
                               tAAAGATACAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACAAGCGGctc                                                                                  >  2:355377/1‑137 (MQ=255)
                                  aGATACATCAAAACGTTT‑AAAAAAAAAACACCCCTCCGCTTCTTTTTGGCCGGCCG‑C‑CTTTTTC‑GCAGCCCTTTTTCTCCCCCCCCGCCCGCACAAAATCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCa                                                                             <  4:218627/139‑1 (MQ=255)
                                      aCAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCCGGCAG‑C‑CTTTTTT‑GCCGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGCCGGCCGATTTGTTTTGTCGCCAACTCGCGGCTCTATCaaa                                                                           >  6:33227/1‑137 (MQ=255)
                                      aCAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGCTTTCTTTTCTCGCAACCGAGCGGCTCTAGCAAAAc                                                                         >  5:373337/1‑139 (MQ=255)
                                      aCAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAAc                                                                         >  8:103549/1‑139 (MQ=255)
                                      aCAAGCAAACGTAT‑CATAGAAAAACATCCCTCCGCTTGTTTTAGGCAGGCCG‑C‑CTTTTTT‑GCAGCCCGTTTTCTCCCCCGCAGCCCGCAAGAAAAGACAGCCCAATAGGTGTCTCGCAAACTAGCGGCTGGACCaaaa                                                                          >  4:189834/1‑138 (MQ=255)
                                        aaGCAAACGTTT‑CATAGAAAAACATCCCTCCGCGTCTTTTTTGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCCGCCGCAGCCCGCAAGAAAAGACGGCCCAGTTCGTTTCTCGCAAACAAGCGGCTCGACCaaacag                                                                        >  1:85066/1‑135 (MQ=255)
                                          gaaaaCGTTT‑CATATAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑CAT‑TTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCCCAATAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                     <  7:307621/137‑1 (MQ=255)
                                          gCAACCGTTT‑CATAGAAAAACCTCCCTCCGCTTCTTTTTGGCCGGCAG‑C‑CTTTTTA‑GCACCCCGTTTGCTCAGCCGCCGCCCGCAACAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                     <  8:386712/139‑1 (MQ=255)
                                          gCAAACTTTT‑AATACAAAAACACCCCTCCGCTTTTTTTGGGCCGGCAG‑C‑C‑TTTTACCCCCCCCGTTTTCTCCCCCCCCGCCCCCAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                     <  1:355377/139‑1 (MQ=255)
                                          gCAAACGTTT‑CATATAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCCGCCGGTTTTCTCACCCGCAGCCCGCAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                     <  3:422918/139‑1 (MQ=255)
                                          gCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                     <  7:275588/139‑1 (MQ=255)
                                          gCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTATTTTCTCGCAAACTAGCGGCTCTAGCCAAACTCAt                                                                     >  6:68866/1‑139 (MQ=255)
                                          ccAAACGTTT‑CATACAAAAACATCCCGCCGCTTCTTTTTGGCCGCCAG‑CAT‑TTTTC‑CCACCCCGTTTTCTCAGCCCCCCCCCCAAATAAACCACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                     <  7:46607/138‑1 (MQ=255)
                                          ccAAACGTGT‑CAAACAAAACCATCCCTCGGGTACTTTTGGCGCGGCAG‑C‑CTTTTTA‑GCACCCGGTTTTCTCCGCCGCTGCCCGCCAGAAAAGACGCCCGATTTATTTTCTCGCAAACAATCGGCTCTAGCAAAACTCAt                                                                     <  6:159651/138‑1 (MQ=255)
                                          caaaaCGTTA‑AATATAAAAACATCCCTCCGCTTCTTTTTGGCAGCCAG‑C‑CTTTTTC‑CCAGCCCGTTTTCACCGCCGCAGCCCGAAATAAAACACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCAt                                                                     <  2:299404/137‑1 (MQ=255)
                                           ccaaCGTTTACAAACAAAAACACCCCTCCGATTTTTTTTGGCGCGCCC‑C‑CTTTTTC‑CCCGCCTGTTTACTCCGCCCCACCCCCCAACAAAACACGGCCGATTTCTTTTCTCGCAAACAAGCGGCTCTAGCAAAACTCAt                                                                     <  6:429304/137‑1 (MQ=255)
                                              aCGTTT‑CATAGAAGAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAcg                                                                 >  2:381336/1‑138 (MQ=255)
                                              aCGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTAGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                 >  5:429304/1‑139 (MQ=255)
                                              aCGTTT‑AATACAAAAACACCCCCCCGCTTCTTTTTGCCTGCCAG‑CTT‑TTTTA‑CCACCCGGTTTTCACCGCCCCAGCCCCAAACAAACGCCGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGAct                                                                 <  7:282206/139‑1 (MQ=255)
                                               cGTTT‑CATAGAAAAACATCCATCCGCTTATTTTTGGCAGGCAGAC‑T‑TTTTA‑GCAGACCGTTTTCTCAGCCGCAGCCCGCAAGAAAATACGGCCGATTTGTTTTCTCCCAAAATAGAGGGTCGAGCAAAACTCATTActc                                                                >  1:139961/1‑139 (MQ=255)
                                                   t‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATTACTCTAt                                                             >  2:286095/1‑138 (MQ=255)
                                                     cATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTAATGACTCTATGa                                                           >  3:98079/1‑139 (MQ=255)
                                                            aaaCATCCCTCCGCTTCTTTTTGGCAGGCAGAC‑T‑TTTTA‑GCAGCCCGATTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTATTTTCTAGCAAACTAGCGGCTCTAGCAAAACTCATGACTCAAAGATAGTCCg                                                    >  8:446484/1‑139 (MQ=255)
                                                                              ttttGGCAGGCCG‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTGTTTTATCGCAAACTAGCGGCGCGCGCAAAACTCATGACTCGATGATAGACCGTGGAAAGAGAATTGtttt                                  >  2:229296/1‑138 (MQ=255)
                                                                               tttGGCAGGCAG‑C‑CTTTTTA‑GCCGCCCGTTTTATCAGCCGCAGCCCGCCAGAAAAGACGGCCGATTTAGTTTATCGCCAACAAACGGCGCTAGCAAAACACAATCCTCTATTAAAGACCCTGGAAAGACAAttaatttt                                 >  4:421995/1‑133 (MQ=255)
                                                                                       gcag‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAatat                         >  5:170270/1‑139 (MQ=255)
                                                                                       gcag‑C‑CTTTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAatat                         >  3:107167/1‑139 (MQ=255)
                                                                                                        agcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTTTCACAATATGAGTGAAAAAAcc            >  3:245560/1‑138 (MQ=255)
                                                                                                         gcCCGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCCTTTCTCGCCAACTAGCGTCTCGAGCAAAACTCATGCCTCAATGATAGACACTGGAAAGCGAAGTCTTTGTCACAATATGAGTGAAAAAACaaa          >  7:358313/1‑139 (MQ=255)
                                                                                                          cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAAc         >  7:271790/1‑139 (MQ=255)
                                                                                                          cccGTTTTCTCAGCCGCAGCCCGCAAGAAAAGACGGCCGAGTTCTTTTCACGCATACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGATAGAGAATTCTTTGTCACAATAAGAGTGAAAAAACCAAc         >  1:249169/1‑139 (MQ=255)
                                                                                                                    cAGCCGCAGCCCGCAAGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGCCTCTATGATAGACCGTGGAAAGAGAATTGTTTGTCACAATATGAGTGAAAAAACCAACTAGtttt  >  8:33294/1‑136 (MQ=255)
                                                                                                                                |                                                                                                                           
CCCAGTTCATCAAAAAGACCATCCACACCCGTAAAGATACAAGCAAACGTTT‑CATAGAAAAACATCCCTCCGCTTCTTTTTGGCAGGCAG‑C‑C‑TTTTA‑GCAGCCCGTTTTCTCAGCCGCAGCCCACGGGAAAAGACGGCCGATTTCTTTTCTCGCAAACTAGCGGCTCTAGCAAAACTCATGACTCTATGATAGACCGTGGAAAGAGAATTCTTTGTCACAATATGAGTGAAAAAACCAACTAGTTTT  >  CP006881/3725114‑3725360

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A