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
A12 F59 I0 R4 226 76.6 2995274 95.4% 2857491 127.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP006881 2,991,176 A→T 39.1% intergenic (‑12/+6) U712_21340 ← / ← U712_21345 tRNA‑Leu/tRNA‑Gly

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0068812,991,1760AT39.1% 13.0 / 6.1 30intergenic (‑12/+6)U712_21340/U712_21345tRNA‑Leu/tRNA‑Gly
Reads supporting (aligned to +/- strand):  ref base A (9/9);  new base T (4/8);  total (13/17)
Fisher's exact test for biased strand distribution p-value = 4.65e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAACGCTCTATCCAATTGAGCTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGATGGTATAGTTGGAGCGGAAGACGGGATTCGAACCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTGCGGATGAAGGGACTTGAACCCCCACGTCTGTAAAGACACTAGAGCC  >  CP006881/2991040‑2991309
                                                                                                                                        |                                                                                                                                     
aaaCGCTCTATCCAATTGAGCTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGATGGTATAGt                                                                                                                                     <  6:195990/139‑1 (MQ=32)
  aCGCTCTATCCAATTGAGCTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGATGGTATAGTTg                                                                                                                                   <  4:200899/139‑1 (MQ=32)
     ctctATCCAATTGAGCTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGATGGTATAGTTGGAg                                                                                                                                <  4:128596/139‑1 (MQ=32)
        tATCCAATTGAGCTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGGTGGGATATTTGGAGCg                                                                                                                              >  5:251935/1‑138 (MQ=12)
          tCCAATTGAGCTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCCCCCCGGCGTGGATGGGATATTTTGGGCgg                                                                                                                             >  6:373398/1‑137 (MQ=11)
            cAATTGAGCTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGATGGTATAGTTGGAGCGGAAGa                                                                                                                         <  5:350378/139‑1 (MQ=32)
               ttGAGCTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGGTGGTATTGTTGGGTCGGGAGACgg                                                                                                                      >  5:267571/1‑139 (MQ=11)
               ttGAGCTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGATGGTATAGTTGGAGCGGTAGACgg                                                                                                                      >  4:103060/1‑139 (MQ=17)
                  aGCTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGGTGGTATTGTTGGAGCGGAAGACgggct                                                                                                                   >  7:28340/1‑137 (MQ=12)
                  aGCTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGGTGGGTTATTTTGTGCGGAAGACGGGAt                                                                                                                   >  3:166562/1‑139 (MQ=11)
                  aGCTACGGGCGCAAAACTTAATGACGAGGGCCGGACTTGAACCCGCACGGTAGTCACCTCCCGCAGGATTTTAAGTCCTGTGTGTCTGCCATTTCCACCACCCCGGCGTGGCGGGTATAATTGGAGCCGCAGCCgggct                                                                                                                   >  2:14023/1‑137 (MQ=11)
                    cTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGATGGTATAGTTGGAGCGGAAGACGGGCTTc                                                                                                                 >  7:85475/1‑139 (MQ=17)
                    cTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGCCGTGGAGGGGATTGTTTGCTCGGAAGCAGGGGTTc                                                                                                                 >  8:358187/1‑139 (MQ=11)
                       cGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGATGGTATAGTTTGGGCGGCAGCCCGGATTCGaa                                                                                                              >  4:51813/1‑139 (MQ=11)
                             cAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGGTGGGATAGTTGTGGCGGAAGACGGGAGTCGCAcacccc                                                                                                        >  7:359611/1‑134 (MQ=11)
                                                                               cgctgtaTTTTAAGTCCTGTGGGGCGGCCAATCCCACCCCCCGGGCGTGGAGGTTATAGTGGGAGCGCAAGCCGGGATTCGACCCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGaa                                                      <  4:32242/133‑1 (MQ=11)
                                                                                      ttttAAGTCGTGTGTGTCGGCCAATTCCACCACCCCGGGGGGGATGGTTTTGTTGGAGCGGAAGACGGGATTCGAACCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTg                                                <  2:328088/138‑1 (MQ=11)
                                                                                      ttttAAGTCCTGTGTGTCTGCCATTTCCCCCACCCCGGGGTTGTTGTTATAGTTGGCGGGGAAGACGGGATTCGAACCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTg                                                <  8:308141/138‑1 (MQ=11)
                                                                                              ccTGTGTGTCTGCAAATTCCACCACCCCGGCGTGGTTGTTTTTGTTGGAGCGTAAGACGGTATTCGAACCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTGCGGATGAAg                                       <  8:359611/139‑1 (MQ=14)
                                                                                                    tgtCTGCCAATTCCACCCCCCCGGCGTGGATGGTATAGTGGGAGCGGAAGCCGGGATTCGAACCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTGCGGATGAAGGGACtt                                 <  3:51813/139‑1 (MQ=255)
                                                                                                     ggcTGCCAAATCCACCCCCCCGGGGGGTTTGGTTATGTTGGAGCTGAACGCGGGAGTCGAACCCGCGACCCCCACCTTGGCAAGGGGGTGTTCTACCACTGAACTACTTCCGAAGAAATGGTGCGGATGAAGGGACTTg                                <  5:373398/137‑1 (MQ=17)
                                                                                                      tCTGCCAATTCCACCACCCCGGCGTGGATGGTATAGTTGGAGCGGAAGACGGGATTCGAACCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTGCGGATGAAGGGACTTGa                               <  8:38709/139‑1 (MQ=255)
                                                                                                             tttCCACCCCCCGGGCGTGGTTTGTATTGTGGGAGCTTAAGAGGGTTTTCGACCCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTGCGGATGAAGGGACTTGAACCCCCa                        <  6:267571/138‑1 (MQ=17)
                                                                                                              ttCCACCACCCCGGCGTGGGTGGTATTGTTGGTGCGGTAGACGGGGTTAGAACCCCCGCCCCCCCCCAGGGCAAGGTTGGGTTGTACCACAGCACGACTTCCGCCGAAAAGGTGGCGTTGAAGGGCCTTGAAccccccc                       >  2:300405/1‑137 (MQ=9)
                                                                                                              tcccaccaCCCGGGGGGGTTTGTTTTTGTTGGCGCGGAAGCCGGGATTCGACCCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTGCGGATGAAGGGACTTGAACCCCCAc                       <  5:347159/137‑1 (MQ=18)
                                                                                                              taccaccaCCCCGGGTGGGATGGTATTGTTGGAGCGCATGACGGGATTCCAACCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTGCGGATGAAGGGACTTGAACCCCCAc                       <  2:94710/137‑1 (MQ=18)
                                                                                                                    ccccccGGGGGTGATGGTTTTGTTGGAGCGCAAGACGGTATTCCAACCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTGCGGATGAAGGGACTTGAACCCCCACGTCTGt                 <  8:246731/137‑1 (MQ=18)
                                                                                                                       cccGGCGTTGATGGTATAGTGGGAGCGGAAGACGGGATGCGAACCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTGCGGATGAAGGGACTTGAACCCCCACGTCTGTaaa              <  5:128793/139‑1 (MQ=255)
                                                                                                                                 aTGGTATAGTTGGAGCGGAAGACGGGATTCGAACCCGCCACCCCCACCTTGGCAAGGTGGTGTTGTACCACAGAACTAATTACCCAGAAATGGTGCGGATGAAGGGTCTTGACCCCCCCCGTCTGTAAAGACACTatag    >  5:128864/1‑139 (MQ=18)
                                                                                                                                    ttataGTTGGTGCGGAAGACGGGATTCGAACCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTGCGGATGAAGGGACTTGAACCCCCACGTCTGTAAAGACACTAGAGcc  <  6:128864/137‑1 (MQ=255)
                                                                                                                                    gTATTGTGGGAGCCGCAGCCGGTTATCGAACCCGCGACCCCCACCTTGGCAAGGTGGTGTTCAACCACTGAACTACTTCCGCAGAAATGGTGCGGATGAAGGGACTAGAACCCCCACGTCTGTAAAGACACTAGAGcc  <  7:293580/138‑1 (MQ=21)
                                                                                                                                        |                                                                                                                                     
AAACGCTCTATCCAATTGAGCTACGGGCGCAAAACTTAATGCCGAGGGCCGGACTTGAACCGGCACGGTAGTCACCTACCGCAGGATTTTAAGTCCTGTGTGTCTGCCAATTCCACCACCCCGGCGTGGATGGTATAGTTGGAGCGGAAGACGGGATTCGAACCCGCGACCCCCACCTTGGCAAGGTGGTGTTCTACCACTGAACTACTTCCGCAGAAATGGTGCGGATGAAGGGACTTGAACCCCCACGTCTGTAAAGACACTAGAGCC  >  CP006881/2991040‑2991309

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A