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
A27 F74 I1 R1 23 45.7 1836232 90.6% 1663626 141.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 696,470 C→T noncoding (35/75 nt) glnX ← tRNA‑Gln

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913696,4700CT96.0% 57.8 / ‑5.8 25noncoding (35/75 nt)glnXtRNA‑Gln
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (9/15);  minor base G (1/0);  total (10/15)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.20e-01

CGTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGC  >  NC_000913/696330‑696607
                                                                                                                                            |                                                                                                                                         
cGTCGCATCCGACATTGAAGGATAAGACGTGTCCACCTCCGAGATACCATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTGTTTTAATGTGGCTGGGGTACGCGGAGTCGAACCTCGCAATGCCGGAATGAg                                                                                                                                         >  2:500334/1‑143 (MQ=255)
 gTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGa                                                                                                                                        <  1:57162/143‑1 (MQ=255)
      ctcggACATTGAAGAATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCg                                                                                                                                   <  2:527737/139‑1 (MQ=255)
       tCCGACATTGAAGGGTAAGACGTGGCAAGATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCGCGCCGAAGCGAGCTTTTTTAACGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCgg                                                                                                                                  <  1:299499/143‑1 (MQ=38)
          gACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGc                                                                                                                               >  2:195104/1‑143 (MQ=255)
                       aaGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAACAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGACCCTCGGAATGCAGGAATTAGAATCCGGTGCCTTACGGCCTgga                                                                                                                  >  2:180476/1‑142 (MQ=37)
                                      cGCATGCGACATTGAATGAACGCAGAAAAGCAAAAAGCGCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTggg                                                                                                   <  2:483729/143‑1 (MQ=255)
                                                    catgaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCCTTCTTAATGCGGCTGGGGTACGAGGCTTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGt                                                                                     <  1:545994/142‑1 (MQ=25)
                                                    aatgaaCGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGAGTGCACTTCCAAGGt                                                                                     >  2:161832/1‑143 (MQ=255)
                                                            cAGAAAAACAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCt                                                                             <  1:241194/143‑1 (MQ=255)
                                                             aGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCtt                                                                            <  1:453478/143‑1 (MQ=255)
                                                                aaaGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGaa                                                                         <  2:371322/143‑1 (MQ=255)
                                                                     aaaaaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGGCAGCACCTTGaagacac                                                                    >  2:272070/1‑138 (MQ=21)
                                                                     aaaaaGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACAGGTTGCACTTACAAGGGAAGCGCGTCGAATaaag                                                                    >  2:484693/1‑142 (MQ=21)
                                                                                   aGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGa                                                      <  1:635321/143‑1 (MQ=255)
                                                                                                 aTGTGGCTGGGGTACGAGGATTCGAGCCTCGGAATGCCGGCATTAGAGTCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCg                                        <  2:284185/143‑1 (MQ=255)
                                                                                                 aTGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCg                                        <  1:195104/143‑1 (MQ=255)
                                                                                                   gtgGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCaa                                                                                                        >  1:163872/1‑77 (MQ=9)
                                                                                                   gtgGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCaa                                                                                                        <  2:163872/77‑1 (MQ=9)
                                                                                                            gTACGAGGATTCGAACCTCGGAATGCCGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGACTGCCGGaa                             >  1:303052/1‑143 (MQ=255)
                                                                                                               cGAGGATGCGAGCCTCGGAATGCCGGGAGTAGAATCCGGTGCCTTACCGCTGGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCa                          <  1:135096/143‑1 (MQ=38)
                                                                                                                          aCCTCGGAATGCCGGAATTAGACACCGGCGCCCCACCTCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGc               <  1:379424/143‑1 (MQ=37)
                                                                                                                                      cGGAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTgg   <  1:702570/143‑1 (MQ=255)
                                                                                                                                       ggAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGGACTTGCAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGGGTGCCGGAATCAGAAGCCGCTGCCTTACCGCTGGGc  >  1:253674/1‑143 (MQ=37)
                                                                                                                                       ggAATTAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGGGCCCTTAAACGGTAAGCGCCATGAATAAAGTGGCTGGGGTAGGAGGATTCGAACGTCGGCATGCCGGAAGCAGAATGCGGTGCCATACGGCTTGGc  >  2:31459/1‑143 (MQ=25)
                                                                                                                                            |                                                                                                                                         
CGTCGCATCCGACATTGAAGGATAAGACGTGTCAACATCGCATTCGACATTGAATGAACGCAGAAAAGCAAAAAGCTCGCCGAAGCGAGCTTTTTTAATGTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGCGATACCCCAACTGGGTGCACTTACAAGGTAAGCGTCTTGAATAAATTGGCTGGGGTACGAGGATTCGAACCTCGGAATGCCGGAATCAGAATCCGGTGCCTTACCGCTTGGC  >  NC_000913/696330‑696607

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A