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
A2 F1 I1 R1 748 32.0 1685426 92.6% 1560704 103.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,614,092 T→C I142I (ATT→ATC)  nikA → nickel/heme ABC transporter periplasmic binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,614,0920TC100.0% 85.9 / NA 25I142I (ATT→ATC) nikAnickel/heme ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (10/15);  total (10/15)

AACCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGG  >  NC_000913/3613962‑3614220
                                                                                                                                  |                                                                                                                                
aaCCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGaa                                                                                                                          <  1:163770/139‑1 (MQ=255)
   cGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAg                                                                                                                       <  1:835395/139‑1 (MQ=255)
                    gcggcAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTcc                                                                                                      >  1:199799/1‑139 (MQ=255)
                             aaCTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGCTTGTTGATGTTAAAGCACTCAGTAAAACGGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                             <  2:513998/139‑1 (MQ=255)
                             aaCTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                             <  1:306022/139‑1 (MQ=255)
                                  ccGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGcc                                                                                        <  1:733402/139‑1 (MQ=255)
                                       cAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGc                                                                                                   <  1:688797/123‑1 (MQ=255)
                                       cAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGc                                                                                                   >  2:688797/1‑123 (MQ=255)
                                         gTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGAAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGcccc                                                                                 >  1:613820/1‑139 (MQ=255)
                                         gTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGAAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGcccc                                                                                 <  2:613820/139‑1 (MQ=255)
                                                     cGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGtt                                                                     <  1:667859/139‑1 (MQ=255)
                                                                               ggCAAACCAGATTGTTGATGTT‑AAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAaaacc                                          >  1:6854/1‑139 (MQ=255)
                                                                                               gATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAgc                                                                                                                      <  1:680175/48‑1 (MQ=255)
                                                                                               gATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAgc                                                                                                                      >  2:680175/1‑48 (MQ=255)
                                                                                                       aGCACTCAGTAAAACAGAGCTGCAAATCACCCTGaaaa                                                                                                                        <  1:680660/38‑1 (MQ=255)
                                                                                                       aGCACTCAGTAAAACAGAGCTGCAAATCACCCTGaaaa                                                                                                                        >  2:680660/1‑38 (MQ=255)
                                                                                                       aGCACTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTaaa                   >  2:416186/1‑139 (MQ=255)
                                                                                                          aCTCAGTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAgcg                <  2:90356/139‑1 (MQ=255)
                                                                                                               gTAAAACAGAGCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGAt           <  2:581044/139‑1 (MQ=255)
                                                                                                                      agagCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCAcc    <  2:199799/139‑1 (MQ=255)
                                                                                                                        agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                             <  1:474369/48‑1 (MQ=255)
                                                                                                                        agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAAc                                                                                             >  2:474369/1‑48 (MQ=255)
                                                                                                                        agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGAt           >  2:650283/1‑130 (MQ=255)
                                                                                                                        agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGAt           <  1:650283/130‑1 (MQ=255)
                                                                                                                        agCTGCAAATCACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCgg  >  1:109685/1‑139 (MQ=255)
                                                                                                                                  |                                                                                                                                
AACCGTTCGATGCCGAGGCGGCGGCAGAAAACTTCCGCGCAGTGCTCGATAACCGTCAACGTCACGCCTGGCTGGAGCTGGCAAACCAGATTGTTGATGTTAAAGCACTCAGTAAAACAGAGCTGCAAATTACCCTGAAAAGCGCCTACTATCCTTTCCTGCAAGAACTGGCCCTGCCCCGTCCTTTCCGTTTTATCGCTCCCTCGCAGTTTAAAAACCATGAAACCATGAACGGAATTAAAGCGCCGATTGGCACCGG  >  NC_000913/3613962‑3614220

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A