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
A1 F1 I1 R1 315 33.5 1889570 98.7% 1865005 80.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,187,691 G→A pseudogene (260/2434 nt) yqiG → putative outer membrane usher protein YqiG

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,187,6910GA100.0% 56.2 / NA 17pseudogene (260/2434 nt)yqiGputative outer membrane usher protein YqiG
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (3/14);  total (3/14)

TTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACT  >  NC_000913/3187616‑3187756
                                                                           |                                                                 
ttAATTGATAACCAAACTGCGGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAaaaa                                                               <  1:598571/80‑1 (MQ=255)
    ttGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTc                                                          <  2:598572/81‑1 (MQ=255)
       aTAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGc                                                       <  2:598573/81‑1 (MQ=255)
          aCCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCaaa                                                    <  1:598575/81‑1 (MQ=255)
          aCCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCaa                                                     <  2:598574/80‑1 (MQ=255)
                  gCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATc                                            >  1:598593/1‑81 (MQ=255)
                     gTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGAt                                         <  2:598576/81‑1 (MQ=255)
                            tGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGgttgtt                                  <  1:598577/81‑1 (MQ=255)
                                acCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTAccc                              <  1:598578/81‑1 (MQ=255)
                                 ccAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCt                             <  1:598579/81‑1 (MQ=255)
                                  cAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTa                            <  1:598580/81‑1 (MQ=255)
                                             aCATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaaaaagaa                 <  1:598581/81‑1 (MQ=255)
                                              cATTATTAGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCgaaaaagaa                 >  1:598596/1‑80 (MQ=255)
                                                   ttaGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATTGTTGTTACCCTATCGAAAAAGAAAAACaa           <  2:598583/81‑1 (MQ=255)
                                                   ttaGGATTTACTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACa            <  1:598582/80‑1 (MQ=255)
                                                            aCTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACt  >  2:598599/1‑81 (MQ=255)
                                                             cTGATGAATTTATTAAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACt  <  2:598584/80‑1 (MQ=255)
                                                                           |                                                                 
TTAATTGATAACCAAACTGCAGTTTGCGTGACACCAGAGCAATTAACATTATTAGGATTTACTGATGAATTTATTGAAAAAACTCAGCAAAACCTGATCGATGGTTGTTACCCTATCGAAAAAGAAAAACAAATTACAACT  >  NC_000913/3187616‑3187756

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A