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
A8 F28 I1 R1 95 36.3 1231394 98.7% 1215385 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 900,696 (A)6→5 intergenic (‑121/+170) artJ ← / ← artM L‑arginine ABC transporter periplasmic binding protein/L‑arginine ABC transporter membrane subunit ArtM

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913900,6910A.93.8% 53.9 / ‑2.1 16intergenic (‑116/+175)artJ/artML‑arginine ABC transporter periplasmic binding protein/L‑arginine ABC transporter membrane subunit ArtM
Reads supporting (aligned to +/- strand):  ref base A (0/1);  new base . (7/8);  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

GGCAAGAACTAACTTTTTCATGATGGAACTCCCGTCTGTCAATCTTATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAATAAAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGCG  >  NC_000913/900555‑900820
                                                                                                                                        |                                                                                                                                 
ggCAAGAACTAACTTTTTCATGATGGAACTCCCGTCTGTCAATCTTATGATTTTTGGCCGTGTCAGCGGCATGGGATAACAATGCGATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAATaaaa                                                                                                                                <  2:612309/140‑1 (MQ=255)
       actaactTTTTCATGATGGAACTCCCGTCTGTCAATCTTATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGa                                                                                                                        <  2:287/140‑1 (MQ=255)
       actaactTTTTCATGATGGAACTCCCGTCTGTCAATCTTATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGa                                                                                                                        <  2:104385/140‑1 (MQ=255)
        ctaactTTTTCATGATGGAACTCCCGTCTGTCAATCTTATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGAc                                                                                                                       <  1:349022/140‑1 (MQ=255)
                                    tGTCAATCTTATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATtat                                                                                           >  2:518875/1‑140 (MQ=255)
                                       cAATCTTATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAg                                                                                        <  2:116603/140‑1 (MQ=255)
                                            ttATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAAttt                                                                                   <  2:329777/140‑1 (MQ=255)
                                               tGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATg                                                                                <  1:589025/140‑1 (MQ=255)
                                                 aTTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCa                                                                              <  1:233528/140‑1 (MQ=255)
                                                 aTTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCa                                                                              <  1:518875/140‑1 (MQ=255)
                                                                    gCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAgg                                                           >  1:445120/1‑140 (MQ=255)
                                                                                   gCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATc                                            >  1:389492/1‑140 (MQ=255)
                                                                                    ccATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATcc                                           >  2:176054/1‑140 (MQ=255)
                                                                                                 ttATATGAAATAAACATGATTAAATAATTTAAATGAAA‑AAAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGCCCCCGCCGCATCCGGCACAGGCACCg                              <  1:45072/140‑1 (MQ=255)
                                                                                                     atGCAATAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCt                          >  1:162285/1‑140 (MQ=255)
                                                                                                           tAAACATGATTAAATAATTTAAATGAAAT‑AAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTc                    >  1:354674/1‑140 (MQ=255)
                                                                                                                          agattAAAATAAAAAAAAAAGCCGGACAATTTAGTGGGTTGTCCGTCTTCATTAAAAGATTTTATGCATTATGTAGGCGGGATAGGGCGCCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTgg      <  2:243815/137‑1 (MQ=255)
                                                                                                                             ttAAATGAAAT‑AAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGcgcg  >  1:64862/1‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                 
GGCAAGAACTAACTTTTTCATGATGGAACTCCCGTCTGTCAATCTTATGATTTTTGGCCGTGTCTGCGGCATGGGATAACAATGCCATCAAGTGAATTTATATGCAATAAACATGATTAAATAATTTAAATGAAATAAAAAAGACGGACAACTTAGTGGGTTGTCCGTCTTCATTATAAGAATTTATGCACTATGTAGGCCGGATAAGGCGTCCCCGCCGCATCCGGCACAGGCACCGTGCTGATGTCTGATGCGACGCTGGCGCG  >  NC_000913/900555‑900820

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A