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 I2 R1 524 31.4 1748232 97.8% 1709770 80.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,679,018 +C coding (350/984 nt) yphF ← putative ABC transporter periplasmic binding protein YphF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,679,0171.C75.0% 38.7 / 10.6 16coding (351/984 nt)yphFputative ABC transporter periplasmic binding protein YphF
Reads supporting (aligned to +/- strand):  ref base . (2/2);  new base C (5/7);  total (7/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAAATTCCAGCGGATCGCCGACCAGATACGCCGAGACATATTTATCGACCCCCTTTTGATTAATACAGGTGTTGTAG‑CAAATCACCGGAATGCCCGCTTCACTGGCGCGACGAACGGTACGGCTACTGCCATTTTCAGACACT  >  NC_000913/2678941‑2679083
                                                                             |                                                                  
cAAATTCCAGCGGATCGCCGACCAGATACGCCGAGACATATTTATCGACCCCCTTTTGATTAATACAGGTGTTGTAG‑Ccaa                                                                <  1:459732/81‑1 (MQ=255)
               cGCCGACCAGATACGCCGAGACATATTTATCGACCCCCTTTTGATTAATACAGGTGTTGTAGCCAAATCACCGGAATGccc                                                  >  2:459755/1‑81 (MQ=255)
                   gACCAGATACGCCGAGACATATTTATCGACCCCCTTTTGATTAATACAGGTGTTGTAGCCAAATCACCGGAATGCCCGCtt                                              <  1:459733/81‑1 (MQ=255)
                      cAGATACGCCGAGACATATTTATCGACCCCCTTTTGATTAATACAGGTGTTGTAGCCAAATCACCGGAATGCCCGCTTCAc                                           <  2:459734/81‑1 (MQ=255)
                        gATACGCCGAGACATATTTATCGACCCCCTTTTGATTAATACAGGTGTTGTAGCCAAATCACCGGAATGCCCGCTTCACTg                                         >  1:459756/1‑81 (MQ=255)
                            cGCCGAGACATATTTATCGACCCCCTTTTGATTAATACAGGTGTTGTAGCCAAATCACCGGAATGCCCGCTTCACTGgcg                                      <  1:459735/80‑1 (MQ=255)
                              ccGAGACATATTTATCGACCCCCTTTTGATTAATACAGGTGTTGTAGCCAAATCACCGGAATGCCCGCTTCACTGGCGcga                                   <  2:459736/81‑1 (MQ=255)
                                   aCATATTTATCGACCCCCTTTTGATTAATACGGGTGTTGTAGCCAAATCACCGGAATGCCCGCTTCACTGGCGCGACGAAc                              <  2:459737/81‑1 (MQ=255)
                                        tttATCGACCCCCTTTTGATTAATACAGGTGTTGTAGCCAAATCACCGGAATGCCCGCTTCACTGGCGCGACGAACGGTa                          <  2:459738/80‑1 (MQ=255)
                                        tttATCGACCCCCTTTTGATTAATACAGGTGTTGTAG‑CAAATCACCGGAATGCCCGCTTCACTGGCGCGACGAACGGTACg                        >  1:459762/1‑81 (MQ=255)
                                         ttATCGACCCCCTTTTGATTAATACAGGTGTTGTAGCCAAATCACCGGAATGCCCGCTTCACTGGCGCGACGAACGGTACg                        >  1:459758/1‑81 (MQ=255)
                                           aTCGACCCCCTTTTGATTAATACAGGTGTTGTAG‑CAAATCACCGGAATGCCCGCTTCACTGGCGCGACGAACGGTACGGc                      >  2:459760/1‑80 (MQ=255)
                                                   ccTTTTGATTAATACAGGTGTTGTAGCCAAATCACCGGAATGCCCGCTTCACTGGCGCGACGAACGGTACGGCTACTGCCa              <  1:459739/81‑1 (MQ=255)
                                                        tGATTAATACAGGTGTTGTAGCCAAATCACCGGAATGCCCGCTTCACTGGCGCGACGAACGGTACGGCTACTGCCAtttt          >  2:459771/1‑80 (MQ=255)
                                                           ttAATACAGGTGTTGTAG‑CAAATCACCGGAATGCCCGCTTCACTGGCGCGACGAACGGTACGGCTACTGCCATTTTCAGac     <  2:459740/81‑1 (MQ=255)
                                                               tACAGGTGTTGTAGCCAAATCACCGGAATGCCCGCTTCACTGGCGCGACGAACGGTACGGCTACTGCCATTTTCAGACACt  >  1:459765/1‑81 (MQ=255)
                                                                             |                                                                  
CAAATTCCAGCGGATCGCCGACCAGATACGCCGAGACATATTTATCGACCCCCTTTTGATTAATACAGGTGTTGTAG‑CAAATCACCGGAATGCCCGCTTCACTGGCGCGACGAACGGTACGGCTACTGCCATTTTCAGACACT  >  NC_000913/2678941‑2679083

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A