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
A9 F59 I0 R1 37 24.7 1037378 89.7% 930528 142.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 710,595 G→T 34.0% P18T (CCT→ACT)  fur ← DNA‑binding transcriptional dual regulator Fur

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913710,5950GT34.0% 13.5 / 14.2 24P18T (CCT→ACT) furDNA‑binding transcriptional dual regulator Fur
Reads supporting (aligned to +/- strand):  ref base G (8/8);  new base T (4/4);  total (12/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.53e-01

AAACTGGTTCAGTACGCGATATACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCC  >  NC_000913/710461‑710737
                                                                                                                                      |                                                                                                                                              
aaaCTGGTTCAGTACGCGATATACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGGTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTa                                                                                                                                        <  2:406592/143‑1 (MQ=255)
 aaCTGTTTCAGTACGCGCTATTCCGTAGCCAGACCCATTTCTTCACCCATATCGATCAGACGTTTGTGTAAATCTTCCGCACTGACGTGTTGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTAc                                                                                                                                       <  1:71591/143‑1 (MQ=255)
  aCTGGTTCAGTACGCGATATACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACt                                                                                                                                      <  1:360344/143‑1 (MQ=255)
      gTTCAGTACGCGCTACCCCGCTTGTAGATCAATTTCGTC‑CCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGCACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAg                                                                                                                                 <  2:385635/143‑1 (MQ=255)
      gTTCAGTACGCGATATACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATACATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGCAGCCCCTCCAGGACTTTTCAACGAGTACGCGTTACTTTCa                                                                                                                                  >  2:511836/1‑143 (MQ=255)
       ttCAGTACGCGATATACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAg                                                                                                                                 >  1:312034/1‑143 (MQ=255)
                         ggaGCGAGACCAGTTTCGTCACCCGTATCGATCGGACGTTTGGATAAGTCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACGTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGc                                                                                                               <  1:36187/141‑1 (MQ=255)
                                   cAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCCGCTCTCTTTAGGGCGGTATGGTTa                                                                                                     >  1:173118/1‑143 (MQ=255)
                                   cAATTTCTTCACCCATATCGATAAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGttg                                                                                                     >  1:99415/1‑142 (MQ=255)
                                      tttCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCCGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCa                                                                                                  >  2:122665/1‑143 (MQ=255)
                                           tcACCCATATCGATAAGACGTTTGTATAAATCTTCCGTACTGACGTGATGGTTGTCAGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTAATTTCAGGCGAGCTTTCTTTAGGGGGGTATTGTGATCAGTCAt                                                                                             >  2:318371/1‑143 (MQ=255)
                                                       aTCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTATACGAGGAATCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTc                                                                                 >  2:33798/1‑143 (MQ=255)
                                                              gTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTGTGGGGCGGTATTGTTATCAAACAGGCGGGAGCTGTCCTGTTAc                                                                          >  1:69113/1‑143 (MQ=255)
                                                              gTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTGTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTCTTGTTATCAGTCATGCGGGATCTGTCCTGttcc                                                                          >  1:168608/1‑141 (MQ=255)
                                                                     taAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCgg                                                                   <  1:474568/143‑1 (MQ=255)
                                                                                cACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCAtt                                                        <  1:133344/143‑1 (MQ=255)
                                                                                 gcTGTCGTGATGGTTGTACGGCTCCTGAAGAACTTCCAGGATTTTTGAACGAGGAAGCGTTACTTTCAGGCCAGCTTTGTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTa                                                       <  2:171386/142‑1 (MQ=255)
                                                                                     aCGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTagaag                                                   <  1:208056/143‑1 (MQ=255)
                                                                                                gTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGACTCTGGCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGaa                                        >  1:490004/1‑143 (MQ=255)
                                                                                                          tGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTg                              >  1:360940/1‑143 (MQ=255)
                                                                                                            aagaaCTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTgag                            <  1:414171/143‑1 (MQ=255)
                                                                                                                   tCCAGGATTTTTCTACGAGGAAGCGTTACTTTCAGTGCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGc                     <  2:300206/143‑1 (MQ=255)
                                                                                                                   tCCAGGATTTTTAAACGAAGAAGCGCTACTTTCAGGCCAGCGTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGc                     <  2:43119/143‑1 (MQ=255)
                                                                                                                     cAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATACTGCGt                   >  1:489915/1‑143 (MQ=255)
                                                                                                                                      gAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGcc  <  1:326618/143‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                              
AAACTGGTTCAGTACGCGATATACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAATTGCC  >  NC_000913/710461‑710737

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A