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
A27 F74 I0 R1 29 16.5 643684 90.6% 583177 142.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,202,409 C→T 23.7% H162Y (CAC→TAC)  zraS → sensory histidine kinase ZraS

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,202,4090CT23.7% 18.5 / 3.9 17H162Y (CAC→TAC) zraSsensory histidine kinase ZraS
Reads supporting (aligned to +/- strand):  ref base C (4/9);  new base T (2/2);  total (6/11)
Fisher's exact test for biased strand distribution p-value = 5.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.60e-01

CGGATGAAATGCAGAAATTAAAGCCAGAGGAAAACTCCCGCTGGCGGCTGCTTGGGAAAACGGAAACTACGCCTGCACTTGAGGTCTATCGTTTGTTCCAGCCAATGTCAGCGCCCTGGCGGCATGGAATGCACAATATGCCGCGCTGTAACGGCAAAGCTGTGCCACAAGTAGATGCACAACAGGCTATTTTTATCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCC  >  NC_000913/4202278‑4202546
                                                                                                                                   |                                                                                                                                         
cgcaTGAAATGCAGGAAGTAAGGCCAGGGGAAGACTCCCGCTGGCGGCTGCCTGGGAAAACGGAAACTACGCCTGCACTTGAGGTCTATCGTTTGTTCCAGCCAAGGTCAGCGCCCTGGCGGCATGGAATGCACAATATGCcg                                                                                                                                <  2:213690/140‑1 (MQ=255)
     gAAATGCAGAAATTAAAGCCAGAGGAAAACTCCCGCTGGCGGCTGCTTGGGAAAACGGAAACTACGCCTGCACTTGAGGTCTATCGTTTGTTCCAGCCAATGTCAGCGCCCTGGCGGCATGGAATGCACAATATGCCGCGCTg                                                                                                                           <  2:277784/143‑1 (MQ=255)
         tGCAGAAATTAAAGCCAGAGGAAAACTCCCGCTGGCGGCTGCTTGGGAAAACGGAAACTACGCCTGCACTTGAGGTCTATCGTTTGTTCCAGCCAATGTCAGCGCCCTGGCGGCATGGAATGCACAATATGCCGCGCTGTAAc                                                                                                                       <  1:189192/143‑1 (MQ=255)
              aaaTTAAAGCCAGAGGAAAACTCCCGCTGGCGGCTGCTTGGGAAAACGGAAACTACGCCTGCACTTGAGGTCTATCGTTTGTTCCAGCCAATGTCAGCGCCCTGGCGGCATGGAATGTACAATATGCCGCGCTGTAACGGCaa                                                                                                                  >  1:149758/1‑143 (MQ=255)
              aaaTTAAAGCCAGAGGAAAACTCCCGCTGGCGGCTGCTTGGGAAAACGGAAACTACGCCTGCACTTGAGGTCTATCGTTTGTTCCAGCCAATGTCAGCGCCCTGGCGGCATGGAATGCACAATATGCCGCGCTGTAACGGCaa                                                                                                                  <  1:20230/143‑1 (MQ=255)
              aaaTTAAAGCCAGAGGAAAACTCCCGCTGGCGGCTGCTTGGGAAAACGGAAACTACGCCTGCACTTGAGGTCTAACGTTAGTGGCGGCGAATGGCAGCGCCCTGGCGGCATGGAATGTACAATATGCCGCGCTGTAACGGCaa                                                                                                                  >  1:318934/1‑143 (MQ=255)
                                                       gAAAACGGAAACTACGCCTGCACTTGAGGTCTATCGTTTGTTCCAGCCAATGTCAGCGCCCTGACGGCATGGACTGCACAATCTGCCGAGCAACAAGGACAAAGGGGTGCAACATACCGGCGTGCAACAGGCTATTTTTagca                                                                         >  1:118565/1‑140 (MQ=255)
                                                                  cTACGCCTGCACTTGAGGTCTATCGCTTGTTCCAGCCAATGTCAGCGCCCTGGCGGCATGGAAGGCACAATATGCCGCGCCGTAACGGCAAAGCTGTGCCACAAGTAGATGCACAACAGGCTATTTTTATCGCCGTTGATGcc                                                              <  1:96679/143‑1 (MQ=255)
                                                                    aCGCCTGCACTTGAGGTCTATCGTTTGTTCCAGACAATGTCAGCGCCCTGGCGGCATGGAATGCACAATATGCCGCGCGGTAACGGCAAAGCGGGACCACAAGGAGAGGCAAAACAGGCTAGTAGTAGCGCCGTTGAAGCCAg                                                            >  2:154221/1‑143 (MQ=255)
                                                                       ccTGCACTTGAGGGCTATCGTTTGTTCCAGCGAATGTCAGCGCCCCGGCAGCATGGAAGGCACAATATGCCGCGATGTAACCGCAAAGCTGTGCCACAAGTAGATGCACAACAGGCTATTTTTATCGCCGTTGATGCCAGTGa                                                         <  2:4747/143‑1 (MQ=255)
                                                                                  ggTCTATCGTTTGTTCCAGCCAATGTCAGCGCCCTGGCGGCATGGAATGCACAATATGCCGCGCTGTAACGGCAAAGCTGTGCCACAAGTAGATGCACAACAGGCTATTTTTATCGCCGTTGATGCCAGTGATCTGGTTGCaa                                              <  1:23207/143‑1 (MQ=255)
                                                                                            ttGTTCCAGCCAATGTCAGCGCCCTGGCGGCATGGAATGCACAATATGCCGCGCTGTAACGGCAAAGCTGTGCCACAAGTAGATGCACAACAGGCTATTTTTATCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTgg                                    <  1:320893/143‑1 (MQ=255)
                                                                                            ttGTTCCAGCCAATGTCAGCGCCCTGGCGGCATGGAATGCACAATATGCCGCGCTGTAACGGCAAAGCTGTGCCACAAGTAGATGCACAACAGGCTATTTTTATCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTgg                                    <  1:191136/143‑1 (MQ=255)
                                                                                                             aGCGCCCTGGCGGCATGGAATGCACAATATGCCGCGCTGTAACGGCAAAGCTGTGCCACAAGTAGATGCACAACAGGCTATTTTTATCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATAccc                   >  1:7940/1‑143 (MQ=255)
                                                                                                                        ggcATGGAATGCACAATATGCCGCGCTGTAACGGCAAAGCTGTGCCACAAGTAGATGCACAACTGGCTATTTTTATCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCctc        >  1:176186/1‑143 (MQ=255)
                                                                                                                              gAATGTACAATATGCCGCGCTGTAACGGCAAAGCTGTGCCACAAGTAGATGCACAACAGGCTATTTTTATCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGcc  <  2:318934/143‑1 (MQ=255)
                                                                                                                              gAATGTACAATATGCCGCGCTGTAACGGCAAAGCTGGGCCACAAGTAGATGCACAACAGGCTATTTTTATCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGcc  <  2:149758/143‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                         
CGGATGAAATGCAGAAATTAAAGCCAGAGGAAAACTCCCGCTGGCGGCTGCTTGGGAAAACGGAAACTACGCCTGCACTTGAGGTCTATCGTTTGTTCCAGCCAATGTCAGCGCCCTGGCGGCATGGAATGCACAATATGCCGCGCTGTAACGGCAAAGCTGTGCCACAAGTAGATGCACAACAGGCTATTTTTATCGCCGTTGATGCCAGTGATCTGGTTGCAACCCAGAGTGGGGAAAAGCGCAATACCCTGATTATCCTCTTCGCC  >  NC_000913/4202278‑4202546

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A