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
A13 F69 I0 R1 1426 148.0 5875178 97.4% 5722423 123.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 285,197 A→G 24.9% intergenic (+29/‑198) yagF → / → yagG CP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913285,1970AG24.9% 54.2 / 12.5 28intergenic (+29/‑198)yagF/yagGCP4‑6 prophage; dehydratase family protein/CP4‑6 prophage; putative sugar transporter
Reads supporting (aligned to +/- strand):  ref base A (10/11);  new base G (2/5);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 6.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCCGGCTGTGGGCGGCACTGCAGTCGGTGAGCGGCGGCACCTGGAAAGGCTGTATTTATGACACCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTCCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAATTAGTTGAGATATATCGTTGGCGTCACAAAAGCAAAATAACGTAATTCGGAAATAAGATATGACCATTGCTGGTTAATTGAATAGCTCATTA  >  NC_000913/285052‑285340
                                                                                                                                                 |                                                                                                                                               
acCCGGCTGTGGGCGGCACTGCAGTCGGTGAGCGGCGGCACCTGGAAAGGCTGTATTTATGACACCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGa                                                                                                                                                 <  1:925088/146‑1 (MQ=255)
acCCGGCTGTGGGCGGCACTGCAGTCGGTGAGCGGCGGCACCTGGAAAGGCTGTATTTATGACACCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGa                                                                                                                                                 >  2:925088/1‑146 (MQ=255)
  ccGGCTGTGGGCGGCACTGCAGTCGGTGAGCGGCGGCACCTGGAAAGGCTGTATTTATGACACCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAGCCGTCTGCGGAATAtt                                                                                                                                            >  2:1232/1‑149 (MQ=255)
  ccGGCTGTGGGCGGCACTGCAGTCGGTGAGCGGCGGCACCTGGAAAGGCTGTATTTATGACACCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAatat                                                                                                                                             <  1:717783/148‑1 (MQ=255)
  ccGGCTGTGGGCGGCACTGCAGTCGGTGAGCGGCGGCACCTGGAAAGGCTGTATTTATGACACCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAatat                                                                                                                                             >  2:717783/1‑148 (MQ=255)
    ggCTGTGGGCGGCACTGCAGTCGGTGAGCGGCGGCACCTGGAAAGGCTGTATTTATGACACCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAat                                                                                                                                               >  2:978772/1‑144 (MQ=255)
    ggCTGTGGGCGGCACTGCAGTCGGTGAGCGGCGGCACCTGGAAAGGCTGTATTTATGACACCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAat                                                                                                                                               <  1:978772/144‑1 (MQ=255)
    ggCTGTGGGCGGCACTGCAGTCGGTGAGCGGCGGCACCTGGAAAGGCTGTATTTATGACACCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTc                                                                                                                                          <  3:198833/149‑1 (MQ=255)
     gCTGTGGGCGGCACTGCAGTCGGTGAGCGGCGGCACCTGGAAAGGCTGTATTTATGACACCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAGCCGTCTGCGGAATATTTcc                                                                                                                                         <  1:1232/149‑1 (MQ=255)
         tgGGCGGCACTGCAGTCGGTGAGCGGCGGCACCTGGAAAGGCTGTATTTATGACACCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGGAAATATTCCGCa                                                                                                                                     <  3:1041753/149‑1 (MQ=255)
                                                               acCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTccc                                                                                                                                        <  1:966569/92‑1 (MQ=255)
                                                               acCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTccc                                                                                                                                        >  2:966569/1‑92 (MQ=255)
                                                                                  tAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTCCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAAt                                                                                             <  3:401709/116‑1 (MQ=255)
                                                                                  tAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTCCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAAt                                                                                             >  4:401709/1‑116 (MQ=255)
                                                                                    aTTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTccc                                                                                                                                        <  4:1341110/71‑1 (MQ=255)
                                                                                    aTTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTccc                                                                                                                                        >  3:1341110/1‑71 (MQ=255)
                                                                                     ttAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTCCCGCAGACGGCTTTGTTGttttt                                                                                                                   <  1:129949/91‑1 (MQ=255)
                                                                                     ttAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTCCCGCAGACGGCTTTGTTGttttt                                                                                                                   >  2:129949/1‑91 (MQ=255)
                                                                                        aCGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTCCCGCAGACGGCttt                                                                                                                            <  3:446943/79‑1 (MQ=255)
                                                                                        aCGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTCCCGCAGACGGCttt                                                                                                                            >  4:446943/1‑79 (MQ=255)
                                                                                                                             agagATAAAACCGTCTGCGGAATATTTCCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAATTAGTTga                                                                                      <  2:168997/80‑1 (MQ=255)
                                                                                                                             agagATAAAACCGTCTGCGGAATATTTCCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAATTAGTTga                                                                                      >  1:168997/1‑80 (MQ=255)
                                                                                                                                         gTCTGCGGGAAATATTCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAATTAGTTGAGATATATCGTTGTCGTCACAAAAGCAAAATAACGTAATTCGGAAATAAGATATGACCATTGCTGGTTAATTGAAt           >  4:871993/1‑143 (MQ=255)
                                                                                                                                         gTCTGCGGGAAATATTCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAATTAGTTGAGATATATCGTTGGCGTCACAAAAGCAAAATAACGTAATTCGGAAATAAGATATGACCATTGCTGGTTAATTGAAt           <  3:871993/143‑1 (MQ=255)
                                                                                                                                         gTCTGCGGAATATTTCCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAATTAGTTGAGATATATCGTTGGCGTCACAAAAGCAAAATAACGTAATTCGGAAATAAGATATGACCATTGCTGGTTAATTGAATAGCTCa     >  3:591214/1‑149 (MQ=255)
                                                                                                                                          tCTGCGGGAAATATTCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAATTAGTTgaga                                                                                    <  3:560576/69‑1 (MQ=37)
                                                                                                                                          tCTGCGGGAAATATTCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAATTAGTTgaga                                                                                    >  4:560576/1‑69 (MQ=37)
                                                                                                                                          tCTGCGGGAAATATTCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAATTAGTTGAGATATATCGTTGGCATCACAAAAGCAAAATAACGTAATTCGGAAATAAGATATGACCATTGCTGGTTAATTGAATAGCTCa     <  4:837402/148‑1 (MQ=255)
                                                                                                                                           cTGCGGGAAATATTCCGCAGACGGTTTTGTTGTTTTTGAAATTTATTAATTTAAACAATTAGtt                                                                                        <  4:559456/64‑1 (MQ=21)
                                                                                                                                            tGCGGAATATTTCCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAATTAGTTGAGATATATCGTTGGCGTCACAAAAGCAAAATAACGTAATTCGGAAATAAGATATGACCATTGCTGGTTAATTGAATAGCTCATTa  <  4:591214/149‑1 (MQ=255)
                                                                                                                                                 |                                                                                                                                               
ACCCGGCTGTGGGCGGCACTGCAGTCGGTGAGCGGCGGCACCTGGAAAGGCTGTATTTATGACACCGATAAAATTATCGAGGTAATTAACGCCGGTAAAAAAGCGCTCGGAATTTAATTATTTTAAGAGATAAAACCGTCTGCGGAATATTTCCCGCAGACGGCTTTGTTGTTTTTGAAATTTATTAATTTAAACAATTAGTTGAGATATATCGTTGGCGTCACAAAAGCAAAATAACGTAATTCGGAAATAAGATATGACCATTGCTGGTTAATTGAATAGCTCATTA  >  NC_000913/285052‑285340

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A