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
A4 F28 I1 R1 128 54.7 1845674 99.3% 1832754 139.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,964,319 (A)7→6 intergenic (‑142/+42) ppdA ← / ← thyA conserved protein PpdA/thymidylate synthase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,964,3130A.100.0% 106.6 / NA 26intergenic (‑136/+48)ppdA/thyAconserved protein PpdA/thymidylate synthase
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (16/10);  total (16/10)

CCGGCAGTATGGAGCGAGGAGAAAAAAAGACGAGGGCCAGTTTCTATTTCTTCGGCGCATCTTCCGGACTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGTAAAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCAATCTCAAAGTCTTCGAAACGGTAGTCGAAGATGGATTCG  >  NC_000913/2964179‑2964448
                                                                                                                                      |                                                                                                                                       
ccGGCAGTATGGAGCGAGGAGAAAAAAAGACGAGGGCCAGTTTCTATTTCTTCGGCGCATCTTCCGGACTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGTaaaaaa                                                                                                                                    <  2:504041/140‑1 (MQ=255)
                 ggagAAAAAAAGACGAGGGCCAGTTTCTATTTCTTCGGCGCATCTTCCGGACTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGt                                                                                                                  <  2:347661/140‑1 (MQ=255)
                   agaAAAAAAGACGAGGGCCAGTTTCTATTTCTTCGGCGCATCTTCCGGACTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCg                                                                                                                >  2:360938/1‑140 (MQ=255)
                        aaaaGACGAGGGCCAGTTTCTATTTCTTCGGCGCATCTTCCGGACTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGct                                                                                                             <  1:113701/138‑1 (MQ=255)
                        aaaaGACGAGGGCCAGTTTCTATTTCTTCGGCGCATCTTCCGGACTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGct                                                                                                             >  2:113701/1‑138 (MQ=255)
                             aCGAGGGCCAGTTTCTATTTCTTCGGCGCATCTTCCGGACTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAg                                                                                                      >  1:353573/1‑140 (MQ=255)
                                        tttCTATTTCTTCGGCGCATCTTCCGGACTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTa                                                                                           <  2:237675/140‑1 (MQ=255)
                                                  ttcGGCGCATCTTCCGGACTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGttt                                                                                               <  2:753425/126‑1 (MQ=255)
                                                  ttcGGCGCATCTTCCGGACTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGttt                                                                                               >  1:753425/1‑126 (MQ=255)
                                                      gcgcATCTTCCGGACTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCAcc                                                                             >  1:848161/1‑140 (MQ=255)
                                                                    cTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGcc                                                               <  2:118136/140‑1 (MQ=255)
                                                                       tttACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCgg                                                            >  2:1722/1‑140 (MQ=255)
                                                                            gCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCg                                                       <  2:603313/140‑1 (MQ=255)
                                                                              cGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGa                                                     <  2:707394/140‑1 (MQ=255)
                                                                                 tGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCg                                                  >  1:266817/1‑140 (MQ=255)
                                                                                      gACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGcc                                             <  2:902353/140‑1 (MQ=255)
                                                                                           tGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCaa                                        >  2:417620/1‑140 (MQ=255)
                                                                                           tGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCaa                                        >  2:58026/1‑140 (MQ=255)
                                                                                           tGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCaa                                        >  1:482367/1‑140 (MQ=255)
                                                                                           tGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGAAAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCaa                                        >  1:700581/1‑140 (MQ=255)
                                                                                                    tCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCAATCTCAAAGt                               <  2:353573/140‑1 (MQ=255)
                                                                                                       ggAAGGCGTCTCGAAGAATTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCAATCTCAAAGTCtt                            >  1:14676/1‑140 (MQ=255)
                                                                                                                        aTTTAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCAATCTCAAAGTCTTCGAAACGGTAGTCGAAg           <  2:705034/140‑1 (MQ=255)
                                                                                                                         tttAACGGAGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCAATCTCAAAGTCTTCGAAACGGTAGTCGAAGa          >  1:799779/1‑140 (MQ=255)
                                                                                                                                 aGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCAATCTCAAAGTCTTCGAAACGGTAGTCGAAGATGGATTCg  >  2:599734/1‑140 (MQ=255)
                                                                                                                                 aGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCAATCTCAAAGTCTTCGAAACGGTAGTCGAAGATGGATTCg  >  1:599370/1‑140 (MQ=255)
                                                                                                                                 aGGGT‑AAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCAATCTCAAAGTCTTCGAAACGGTAGTCGAAGATGGATTCg  >  1:307576/1‑140 (MQ=255)
                                                                                                                                      |                                                                                                                                       
CCGGCAGTATGGAGCGAGGAGAAAAAAAGACGAGGGCCAGTTTCTATTTCTTCGGCGCATCTTCCGGACTATTTACGCCGTTGCAGGACGTTGCAAAATTTCGGGAAGGCGTCTCGAAGAATTTAACGGAGGGTAAAAAAACCGACGCACACTGGCGTCGGCTCTGGCAGGATGTTTCGTAATTAGATAGCCACCGGCGCTTTAATGCCCGGATGCGGATCGTAGCCTTCAATCTCAAAGTCTTCGAAACGGTAGTCGAAGATGGATTCG  >  NC_000913/2964179‑2964448

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A