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 F3 I95 R1 196 14.2 808436 96.0% 776098 85.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NZ_CP009273 1,673,542 A→G K287E (AAG→GAG)  ydgH → DUF1471 family protein YdgH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NZ_CP0092731,673,5420AG88.9% 11.2 / ‑3.6 9K287E (AAG→GAG) ydgHDUF1471 family protein YdgH
Reads supporting (aligned to +/- strand):  ref base A (1/0);  new base G (1/7);  total (2/7)
Fisher's exact test for biased strand distribution p-value = 2.22e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.99e-01

GGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATC  >  NZ_CP009273/1673460‑1673617
                                                                                  |                                                                           
ggTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAgg                                                                      >  1:22836/1‑90 (MQ=255)
    ccGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCt                                                                  <  2:37771/90‑1 (MQ=255)
     cGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTa                                                                 <  2:219998/90‑1 (MQ=255)
      gTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTaa                                                                <  1:175094/90‑1 (MQ=255)
                                      gCAACATGCCCGAAGTCTCCTATCAGGTTGCGAAAGGGGCCGGGGAGAAGGGTGCTAAGTATTACCACATCCCCCGCCAGTGGCAGGAAc                                <  2:91363/90‑1 (MQ=255)
                                        aaCATGACCGAAGTCCCCTATCGGGTTGGAAAGCGTGCCGCGGAGAAAGGTGCTAAGTTTTCCCACACCCCCCGCCAGTGGCAGGAACGt                              <  2:170550/90‑1 (MQ=255)
                                        aaCAGGCCCGAAGTCTCCTATCGGGTTGCGAAACGGGCCGGGGAGAAGGGTGCTAAGTATTCCCACACCCCCCGCCAGTGGCAGGAACGt                              <  2:153234/90‑1 (MQ=255)
                                                                  tGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGa    >  1:284539/1‑90 (MQ=255)
                                                                    cGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATc  <  1:143645/90‑1 (MQ=255)
                                                                                  |                                                                           
GGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATC  >  NZ_CP009273/1673460‑1673617

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

BRESEQ :: bam2aln output
CAGCGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATA  >  NZ_CP009273/1673450‑1673627
                                                                                            |                                                                                     
CAGCGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGG                                                                                >  SRR3722235.23107/1‑100 (MQ=60)
CAGCGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGG                                                                                <  SRR3722235.64560/100‑1 (MQ=60)
                tacgagattgcctcttgtctcgcgggctcggagatgtgtataagagacagCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCAC                                                                <  SRR3722235.372590/50‑1 (MQ=60)
                GTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCAC                                                                <  SRR3722235.177103/100‑1 (MQ=60)
                                                                  CCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGA              >  SRR3722235.288462/1‑100 (MQ=60)
                                                                              CGAAACGTGCCGCGGAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATA  <  SRR3722235.145301/100‑1 (MQ=60)
                                                                                            |                                                                                     
CAGCGATGATGGTCCCGTTCGACAGCATCAAATTCTCTGGCAACTACGGCAACATGACCGAAGTCTCCTATCAGGTTGCGAAACGTGCCGCGAAGAAAGGTGCTAAGTATTACCACATCACCCGCCAGTGGCAGGAACGTGGTAATAACCTGACCGTCAGCGCAGATCTGTATAAATA  >  NZ_CP009273/1673450‑1673627

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑