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 F58 I1 R1 20 92.2 2125266 63.9% 1358044 150.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP000730 584,121 G→T intergenic (+205/‑67) rplA → / → rplJ ribosomal protein L1/ribosomal protein L10

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730584,1210GT95.7% 143.5 / ‑0.6 46intergenic (+205/‑67)rplA/rplJribosomal protein L1/ribosomal protein L10
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base T (30/14);  total (31/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

ATTGACAATAAGTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAATTCAGTTTCAACAGTA  >  CP000730/583973‑584265
                                                                                                                                                    |                                                                                                                                                  
atTGACAATAAGTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTg                                                                                                                                                  >  2:83513/1‑151 (MQ=255)
  tGACAATAAGTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTggg                                                                                                                                                >  1:601644/1‑151 (MQ=255)
   gACAATAAGTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCGTGGGt                                                                                                                                               <  2:642298/151‑1 (MQ=255)
          aGTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGt                                                                                                                                        <  2:965124/151‑1 (MQ=255)
             aaTTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCt                                                                                                                                     <  2:432115/151‑1 (MQ=255)
                        tataTTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTaa                                                                                                                          >  1:815794/1‑151 (MQ=255)
                             tACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTa                                                                                                                    >  2:23877/1‑151 (MQ=255)
                                  aTTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTaaaaaa                                                                                                               >  1:993432/1‑151 (MQ=255)
                                     gtgATTATTTTACCTAAGACAGTAGGAGTTATTTAGAACTTAAAATTTTGCCTGCCTAGGCTAAAATTTACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAGGGGCTTTTTTTATTAATT‑TTAAAAAAAGc                                                                                                            >  2:635927/1‑151 (MQ=255)
                                              ttACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTA‑AAATTAATAAAAAAAGCActttctac                                                                                                   <  1:468520/151‑8 (MQ=38)
                                                aCCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAAttt                                                                                                 >  1:751415/1‑151 (MQ=255)
                                                         aGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAgg                                                                                        <  1:302345/151‑1 (MQ=255)
                                                                gTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTTTTTTTTTTTTAAAGTGCTTTTTTTATTAATT‑TTAAAAAAATCATCAATTATTTAAATGGAGGTGTCTGa                                                                                 >  2:466054/1‑151 (MQ=255)
                                                                  tatttatAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTTTTTTTTTTTTAAAGTGCTTTTTTTATTCATT‑TTAATAAATGCACCAAAAATTTAAATGGTGGTGTCTGCAt                                                                               >  2:211796/1‑151 (MQ=255)
                                                                  tatttatAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAAt                                                                               >  1:853071/1‑151 (MQ=255)
                                                                    tttatAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGt                                                                             >  2:613999/1‑151 (MQ=255)
                                                                        taACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTTCTTTTTTTTTAAAGTGCTTTTTTTATTAATT‑TTAAAATAAGCACCAAAAATTTAAATGGAGGTGTCTGCCTGTCTGc                                                                         >  2:394297/1‑151 (MQ=255)
                                                                          aCTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTa                                                                       >  2:217920/1‑151 (MQ=255)
                                                                           cTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTAt                                                                      >  2:710087/1‑151 (MQ=255)
                                                                            ttAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATc                                                                     <  1:905288/151‑1 (MQ=255)
                                                                               aaaTTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCAtt                                                                  <  1:23877/151‑1 (MQ=255)
                                                                                aaTTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTGGGGTAGAAAGTGCTTTTTTTATTAATT‑TTACAAAAAGCACCAAAAATTCAAATTGAGGGGTCTGAATGTCTGCTATCAttt                                                                 >  2:621747/1‑150 (MQ=255)
                                                                                aaTTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGTAGGTGTCTGAATGTCTGCTATCATTg                                                                 >  2:344821/1‑151 (MQ=255)
                                                                                 aTTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGa                                                                >  1:353050/1‑151 (MQ=255)
                                                                                  tttATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGaa                                                               >  2:380343/1‑151 (MQ=255)
                                                                                         tGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑aaaa                                                       >  2:585815/1‑151 (MQ=255)
                                                                                          gCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTTTTTTTT‑TTAAAAAAAGCACCAAAAATTTAAATGTAGTTGTCTGAATGTCTGCTATCATTGAAGCT‑aaaaa                                                      >  2:363101/1‑151 (MQ=255)
                                                                                             gAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAaaca                                                   <  2:993432/151‑1 (MQ=255)
                                                                                               ggCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAaacaac                                                 <  2:663756/151‑1 (MQ=255)
                                                                                               ggCTAAAATGGAATTGAACGTGATGATATATGATCTTTCAAGCAATTTTTGCATTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAATTGGAGGTGTCTGATTTTCTTCTATCATTAAAGCT‑AAAAaacaac                                                 <  2:96465/151‑1 (MQ=255)
                                                                                                 cTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCTAAAAAAACAACt                                                >  1:212863/1‑151 (MQ=255)
                                                                                                  tAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAg                                              >  1:868162/1‑151 (MQ=255)
                                                                                                           cTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAGTTGATGaaa                                     >  1:613158/1‑151 (MQ=255)
                                                                                                               aaCGTGATGATCTATGATCTTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAGTTGATGAAATTGc                                 <  2:650608/151‑1 (MQ=255)
                                                                                                                          ctatgatctTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTATTTTATTAATT‑TTAAAAAAAGCACAAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAAATAGATGATGAAATTGCTGAGGTACTAt                      >  1:496676/1‑151 (MQ=255)
                                                                                                                           tatgatctTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATc                     >  1:608753/1‑151 (MQ=255)
                                                                                                                              gatctTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCaaaaa                                                                                                    >  2:1020356/1‑70 (MQ=255)
                                                                                                                              gatctTTCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCaaaaa                                                                                                    <  1:1020356/70‑1 (MQ=255)
                                                                                                                                  tttCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTATTT‑TTATAAAAAGCACTAAAATTTTAAATTGTGGTGTTTGAATGTCTGCTATCATTTAAGCT‑AAAAAACAACTAGTTGATTAAATTGCTGAGGTACTATCAAATTCa              >  2:282695/1‑151 (MQ=255)
                                                                                                                                  tttCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAGTTGATGAAATTGc                                 >  1:208630/1‑132 (MQ=255)
                                                                                                                                  tttCAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAGTTGATGAAATTGc                                 <  2:208630/132‑1 (MQ=255)
                                                                                                                                     cAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAATTCAGtt           >  1:393810/1‑151 (MQ=255)
                                                                                                                                     cAAGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAATTCAGtt           <  2:815794/151‑1 (MQ=255)
                                                                                                                                       aGCACTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAATTCAGTTTc         >  1:746255/1‑151 (MQ=255)
                                                                                                                                          aCTTTTTGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAATTCAGTTTCAAc      >  1:889380/1‑151 (MQ=255)
                                                                                                                                              tttGCCTTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAATTCAGTTTCAACAGTa  <  1:411156/151‑1 (MQ=255)
                                                                                                                                                    |                                                                                                                                                  
ATTGACAATAAGTAATTTCCAAGTTATATTACTTATTGTGATTATTTTACCTAAGACAGTAGGAGTTATTTATAACTTAAAATTTATCCTGCCGAGGCTAAAATTGACTTGAACGTGATGATCTATGATCTTTCAAGCACTTTTTGCCGTGGGTAGAAAGTGCTTTTTTTATTAATT‑TTAAAAAAAGCACCAAAAATTTAAATGGAGGTGTCTGAATGTCTGCTATCATTGAAGCT‑AAAAAACAACTAGTTGATGAAATTGCTGAGGTACTATCAAATTCAGTTTCAACAGTA  >  CP000730/583973‑584265

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ 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