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
A19 F91 I0 R1 49 33.8 1296440 89.8% 1164203 142.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 710,595 G→T 100% 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_000913710,5950GT100.0% 105.8 / ‑6.7 38P18T (CCT→ACT) furDNA‑binding transcriptional dual regulator Fur
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base T (22/15);  total (22/16)
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.

TCAAACTGGTTCAGTACGCGATATACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAA  >  NC_000913/710459‑710732
                                                                                                                                        |                                                                                                                                         
tcAAACTGGTTCAGTACGCGATATACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGt                                                                                                                                     >  2:465844/1‑143 (MQ=255)
 cAAACTGGTTCAGTACGCGATATACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGtt                                                                                                                                    <  1:346444/143‑1 (MQ=255)
         ttCAGTACGCGATATAGCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAg                                                                                                                            <  2:442703/143‑1 (MQ=255)
                    atatACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGctttct                                                                                                                 >  1:192299/1‑143 (MQ=255)
                     tataCCGTAGCCAGACCAACTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGctttctt                                                                                                                <  2:117806/143‑1 (MQ=255)
                       tcccGTACCCAGACCAATTTCTTCCCCCATATCGATCCGCCGTTTTTATACATCTTCCGCACTGACGTGATGGTTTTCCGGCCCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTa                                                                                                              <  1:127171/141‑1 (MQ=255)
                       taCCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATACATCTTCCGCACTGCCGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGGGTTATTTTAAGGCCCGctttatcta                                                                                                              >  1:20267/1‑138 (MQ=255)
                                    ccAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGtt                                                                                                 <  2:619529/143‑1 (MQ=255)
                                        tttCTTCACCCATATCGATCAGTCGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGCAGAACTTCCATGATTTTTACGCGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCa                                                                                             <  2:233631/143‑1 (MQ=255)
                                        tttCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTACTTTAGGGCGGTATTGTTATCa                                                                                             >  1:86949/1‑143 (MQ=255)
                                        tttCTTCACCCAGAGCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGGTGTCCGGCTCCTGAAGAACGTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCa                                                                                             <  2:200474/143‑1 (MQ=255)
                                             tcACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTCATGGTCGTCCGGCTCCCGCAGCACTCCAAGCATTTTTATACGAGTAAGCGTTACTTTCAGGCCAGCTCTCTGTAGGGCGGTATTCTTATCAGtagt                                                                                        >  2:225930/1‑140 (MQ=255)
                                                  cATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGa                                                                                   <  1:31376/143‑1 (MQ=255)
                                                   atatCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGaa                                                                                  >  1:81883/1‑143 (MQ=255)
                                                         aTCAGACGTTTGTATCAATCTTCCGCACTGACGTTATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTc                                                                            <  2:642858/143‑1 (MQ=255)
                                                          tCAGACGGGTGTATAAACCTTCCGCACTGGCGTGAGGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTcc                                                                           <  1:434624/143‑1 (MQ=255)
                                                                      ataAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATGTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTGAAGGGGGAATTGTTATCAGTCAGGCGGAATCTGTCATGTGATTAAACg                                                               >  2:171988/1‑143 (MQ=255)
                                                                         aaTCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATCTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGtt                                                            >  1:489183/1‑143 (MQ=255)
                                                                                 ggattGACGTGATGGTTGTCCGGCTCCTGATGATCTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGTTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCAt                                                    <  2:17419/139‑1 (MQ=255)
                                                                                  cACGGACGGGATGGTTGTCCGGTTCCTGAAGAACTGCCAGGAGTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCAtt                                                   <  2:358361/143‑1 (MQ=255)
                                                                                     tGACGTGATGGTGGTCCGGCTCCCGAAGAACTTCCAGGAGTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTaga                                                <  2:280749/143‑1 (MQ=255)
                                                                                        cGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTagaaga                                             >  1:163787/1‑143 (MQ=255)
                                                                                          tGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTTCTCAGCGGTTCCCTTCATTAGaagaag                                           >  1:563850/1‑143 (MQ=255)
                                                                                                 tGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGCATTGTTATCAGTCACGCGGGATCTGCCCTGTTACTAAGCGGTTCACTTCATTAGACGAAGTGACAGa                                    >  1:119723/1‑143 (MQ=255)
                                                                                                 ggTCCGCCTGCTGAAGAACTTCCAGGATTGTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGa                                    <  2:68206/142‑1 (MQ=255)
                                                                                                   tCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTGAGGCCAGCTTTCTTTAGGGCGGGATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGGAt                                  >  1:129570/1‑143 (MQ=255)
                                                                                                   tCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACGGagt                                  >  1:62931/1‑141 (MQ=255)
                                                                                                   tCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGact                                  >  2:33171/1‑141 (MQ=255)
                                                                                                    ccGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAAtt                                 <  1:302381/143‑1 (MQ=255)
                                                                                                       gCTCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTACTGTTATCAGTCATGCCGCATCTGTCCTGTTACCAAGCGGGTCACATACTTCGAAGCAGTGACTGAATTTGc                              >  2:99176/1‑143 (MQ=255)
                                                                                                         tCCTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGctc                            >  2:435053/1‑143 (MQ=255)
                                                                                                           cTGAAGAACTTCCAGGATTTTTAAACGAGTAAGCGTTACTGTCAGGCCAGCGTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATAACAAGAAGTGCCAGAATTTGCTCtt                          >  2:168009/1‑143 (MQ=255)
                                                                                                             ggagaaCTTCCAGGATTTTTAAACGAGGTAGTGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTga                        <  2:346155/141‑1 (MQ=255)
                                                                                                             gaagaaCTTCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTga                        >  1:560837/1‑143 (MQ=255)
                                                                                                                    ttCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTGCTGAGCGGTTCACTTCCTTGGCAGAAGTGCCAGACTTTGCTCTGGAGTTAATg                 >  2:310239/1‑143 (MQ=255)
                                                                                                                    ttCCAGGATTTTTAAACGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATg                 >  2:244923/1‑143 (MQ=255)
                                                                                                                                  aaCGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGCAGTGACAGAATTTGCTCTTGAGATAATGCGAAACAATATAGa   >  1:561040/1‑143 (MQ=255)
                                                                                                                                   aCGAGTAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGaa  >  2:432939/1‑143 (MQ=255)
                                                                                                                                        |                                                                                                                                         
TCAAACTGGTTCAGTACGCGATATACCGTAGCCAGACCAATTTCTTCACCCATATCGATCAGACGTTTGTATAAATCTTCCGCACTGACGTGATGGTTGTCCGGCTCCTGAAGAACTTCCAGGATTTTTAAACGAGGAAGCGTTACTTTCAGGCCAGCTTTCTTTAGGGCGGTATTGTTATCAGTCATGCGGAATCTGTCCTGTTACTAAGCGGTTCACTTCATTAGAAGAAGTGACAGAATTTGCTCTTGAGATAATGCGTATCATTATAGAA  >  NC_000913/710459‑710732

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