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 F178 I0 R1 41 49.4 1100758 95.6% 1052324 140.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,028,583 G→T 100% A21D (GCC→GAC)  USA300HOU_RS10230 ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,028,5830GT96.1% 100.6 / ‑4.2 41A21D (GCC→GAC) USA300HOU_RS10230hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (1/1);  new base T (17/21);  total (19/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCA  >  USA300TCH1516_ALE/2028449‑2028719
                                                                                                                                       |                                                                                                                                        
aTAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCaata                                                                                                                                     <  1:517227/140‑1 (MQ=255)
        ccTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTAAATAAACTACTACAGATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATGTGTAGTAAAAATTGTCAATAATCATTaa                                                                                                                             >  2:253/1‑140 (MQ=255)
         cTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTATAAATAAtaattaat                                                                                                                            >  1:398648/1‑140 (MQ=255)
                      cAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACGCATCCCACTAATAGAACGAGTAAAAAGCCAAT‑TTTGTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCCGTAAAAATGa                                                                                                               >  2:39976/1‑140 (MQ=255)
                        aaaGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATc                                                                                                             <  1:187938/140‑1 (MQ=255)
                          aGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCaa                                                                                                           >  1:491044/1‑140 (MQ=255)
                          aGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGAACaa                                                                                                           >  2:395975/1‑140 (MQ=255)
                          aGGCCACATATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGAAGTAAAAATTGTCAATAATCATTAATGCAGTACAAATGATCaa                                                                                                           >  1:343601/1‑140 (MQ=255)
                              caactATGTTATGAAAATAAAGATATCCTACATAAACTAATACACATCACAATTATACAACTAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACAtt                                                                                                       <  1:128125/136‑1 (MQ=255)
                              cACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACAtt                                                                                                       <  2:338193/140‑1 (MQ=255)
                              cACGTATTTTATGAAAATAAAGATATACTACATTAACCAATACACATCCCAATAATAGAACGACTAAAAAACCAAA‑ATATTCAAATAATATGTAGTAAAAATTGTCAATAATCATTAATGTAGTAAAAATGATCAACAtt                                                                                                       <  1:357858/140‑1 (MQ=255)
                              cACGTACTTTATGAAAATAAAGATATCCTACATAAACTATTTCAGACTCCACTATTAGAAGTAGTAAAAAGTCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACAtt                                                                                                       <  2:30991/140‑1 (MQ=255)
                                cGTATTTTATGATAATAAAGATATTCTTCATAAACTAATACACATCGCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTg                                                                                                     <  1:232385/140‑1 (MQ=255)
                                      ttattaAAATAAAGATATCCTACTTAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCAAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGa                                                                                               <  1:132610/140‑1 (MQ=255)
                                        atcacaaTAAAGATATCCTACATCATCTAATAAACATCCCAATAATTGAACGAATAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATTTTCAACATGTGCGTTGata                                                                                             <  2:242340/135‑1 (MQ=255)
                                        aTGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGata                                                                                             <  1:390130/140‑1 (MQ=255)
                                               gaaaGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TATTACAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATAttt                                                                                      <  2:264474/139‑1 (MQ=255)
                                                aaaGATTACCTACATAAACTAACACACATCCCAATAATAGAACGAGTAAAAAGCCAAA‑AATAAAAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTtg                                                                                     <  2:447065/140‑1 (MQ=255)
                                                     tatCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATGGTCAATAAAAACAAAATCAGTAAAAATGATCAACATTTGCGTTGGAAGATATTggtgtat                                                                                >  1:345153/1‑138 (MQ=255)
                                                          tACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGGTGATAAATATTTGGTTGTCATGt                                                                           >  2:233307/1‑140 (MQ=255)
                                                          tACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATAAACATTTGCGTTGATATATATTTGTGTGTAATGt                                                                           >  2:470560/1‑140 (MQ=255)
                                                           aCATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTTTTATTTTTTGTAGTAAAAATAGTCAATAATCATTAATACGGTCAAAATGCTCGACATTCGCGTTGACATATATTTGAGAGTcccgct                                                                          >  2:95249/1‑135 (MQ=255)
                                                           aCATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TGTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTACTGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGtt                                                                          <  1:105905/140‑1 (MQ=255)
                                                              tAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTcg                                                                       <  1:508388/140‑1 (MQ=255)
                                                              tAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTcg                                                                       <  1:228842/140‑1 (MQ=255)
                                                              aaaaCTAAAAAGCATCCCAAAAATAGAAAGAGTAAAAAGCAAAA‑ATAAAAAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTcg                                                                       <  2:398648/139‑1 (MQ=255)
                                                               aaaCTAATACCTATCCCAATAATACAACGAGTAAACAGCAAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAAGGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTcgc                                                                      <  2:449112/140‑1 (MQ=255)
                                                               aaaCTAATACACATCCAAATAATAGTACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCACTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTcgc                                                                      <  1:332477/140‑1 (MQ=255)
                                                                        cacaTCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATTTACATGCGTTTGTCATGTTTCGCCGCCctttt                                                             >  2:524810/1‑138 (MQ=255)
                                                                        cacaTCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCt                                                             >  1:229206/1‑140 (MQ=255)
                                                                             ccaactaaaaGAACGAAGAAAACCCCAAA‑TTCTTCAAAAAATATGTAGTAAAAATTGTCGATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGcc                                                        <  1:283669/135‑1 (MQ=255)
                                                                              ccAATAATAGAACAAGTTAAATGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCca                                                       <  2:272088/140‑1 (MQ=255)
                                                                                aataatAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCcaca                                                     >  2:372549/1‑140 (MQ=255)
                                                                                aataatAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCcaca                                                     <  1:120715/140‑1 (MQ=255)
                                                                                  taataGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTATGTCATGTTTCGCCGCCTTTCTATACCCCAGc                                                   >  1:183982/1‑140 (MQ=255)
                                                                                       gAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCa                                              >  1:33599/1‑140 (MQ=255)
                                                                                               caaaaGCCAAT‑ACTTTCGACAAAGCGGTAGTAAAAATTGCCAATAATCATTAATGCAGTCAAAATGATCAACATTTGCTGTTATATATATGTGTGTGTCATGTTTCGCCGCCTTTCTATGCAACATCGGTCatatctttt                                      >  2:538574/2‑135 (MQ=255)
                                                                                               aaaaaGCCAAT‑TTTTTCAAAGAATTTGTAGTAAAAATAGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCGACAGCCTTCATATAAttt                                      >  2:119925/1‑140 (MQ=255)
                                                                                                aaaaGCCAATATTTTTTTTAAAAT‑TGAAGTAAAAATGGGCAATAATCATTAATCCAGTAAAAATGATCAACATTTGCGTTGTTATATATTTGTGTGTACTGTTTGGACGGTATGCTATTCTACAGCGTTCATATAATtta                                     >  2:113844/1‑140 (MQ=255)
                                                                                                    gCCAAT‑TTTTTCAAAAAATATGTAATAAAAATTGTCAATAATCATAAATGCAGTAAAAATGATCAACATTTGCGTTGATATATAATTGTGTGGCGTGTTTCGCCGCCTTTCTATGCCAAATCGTTGATATAattaattaa                                 >  2:226908/1‑139 (MQ=255)
                                                                                                                                    ttGTCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCa  <  1:233307/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                        
ATAGCGCGCCTATCCAAAACGCCAAAAGGCCACGTATTTTATGAAAATAAAGATATCCTACATAAACTAATACACATCCCAATAATAGAACGAGTAAAAAGCCAAT‑TTTTTCAAAAAATATGTAGTAAAAATTGGCAATAATCATTAATGCAGTAAAAATGATCAACATTTGCGTTGATATATATTTGTGTGTCATGTTTCGCCGCCTTTCTATGCCACAGCGTTCATATAATTTATTAGATACGATGTTTTTTCTGTTGCTATTTTTTCA  >  USA300TCH1516_ALE/2028449‑2028719

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A