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
A6 F1 I1 R1 750 51.0 2595496 93.6% 2429384 106.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,139,406 Δ1 bp coding (1029/1644 nt) flgK → flagellar hook‑filament junction protein 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,139,4060T.100.0% 53.5 / NA 14coding (1029/1644 nt)flgKflagellar hook‑filament junction protein 1
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (6/8);  total (6/8)

CTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGGTGACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTACGGTGACGCCGG  >  NC_000913/1139284‑1139536
                                                                                                                          |                                                                                                                                  
cTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGc                                                                                                                   >  2:793957/1‑139 (MQ=255)
  ggCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCa                                                                                                                 >  2:1078764/1‑139 (MQ=255)
                                        gATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACATTGCGAt                                                                                                                         <  1:924862/93‑1 (MQ=255)
                                        gATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACATTGCGAt                                                                                                                         >  2:924862/1‑93 (MQ=255)
                                        gATTTGATGCTAACGGCGATGACGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTAc                                                                           <  2:801702/139‑1 (MQ=255)
                                         aTTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACa                                                                          <  1:566575/139‑1 (MQ=255)
                                                        cGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGtt                                                                >  1:1099680/1‑134 (MQ=255)
                                                        cGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGtt                                                                <  2:1099680/134‑1 (MQ=255)
                                                                          cTTTGCTATAGGTAAGCCCGCGGGTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGGTCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGAGTACGAAATCTCGTTCGATAATAATCAGTGGCAGTTCa                                         <  2:484579/139‑1 (MQ=255)
                                                                                 aTCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCcg                                                                                               <  1:757873/78‑1 (MQ=255)
                                                                                 aTCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCcg                                                                                               >  2:757873/1‑78 (MQ=255)
                                                                                            cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGc                                                                                                    <  1:1188103/62‑1 (MQ=255)
                                                                                            cgcgGTTCTGCAAAACACGAAAAACAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGc                                                                                                    >  2:1188103/1‑62 (MQ=255)
                                                                                                                 aaaCAAAGG‑GACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTACGGTGACGCCgg  <  1:793957/139‑1 (MQ=255)
                                                                                                                          |                                                                                                                                  
CTGGCATTTGCCGAGGCTTTCAACACCCAACACAAAGCCGGATTTGATGCTAACGGCGATGCCGGTGAAGATTTCTTTGCTATCGGTAAGCCCGCGGTTCTGCAAAACACGAAAAACAAAGGTGACGTTGCGATCGGTGCCACGGTAACTGATGCCTCCGCGGTACTGGCGACAGATTACAAAATCTCGTTCGATAATAATCAGTGGCAGGTCACCCGCCTTGCCAGCAATACCACTTTTACGGTGACGCCGG  >  NC_000913/1139284‑1139536

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A