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
A5 F43 I1 R1 6 69.6 3402438 93.9% 3194889 134.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_002947 4,741,280 C→T intergenic (+471/+281) gltA → / ← yeiW citrate synthase/putative oxidoreductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0029474,741,2800CT79.5% 74.0 / 13.2 39intergenic (+471/+281)gltA/yeiWcitrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand):  ref base C (7/1);  new base T (14/17);  total (21/18)
Fisher's exact test for biased strand distribution p-value = 4.89e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

TCTTCTTTCAGGTTACGGGTCAGGCTGCCATCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AA‑CC‑TCC‑GCCAAC‑TGCATTCGTGAA‑CCAAGCAACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACT  >  NC_002947/4741137‑4741410
                                                                                                                                                  |                                                                                                                                     
tcttctTTCAGGTTACGGGTCAGGCTGCCCTCCGCCTCCTTGGTGGTCGTAATGTGCAGCACGGACTCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCCCTGGTCACCGTCGTGCTTGAG‑CA‑GC‑Tcctgcgac                                                                                                                                 >  2:187952/1‑144 (MQ=255)
                                cGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGa                                                                                               <  1:993400/150‑1 (MQ=255)
                                 gCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGATCAAGTCAACTGCGGCTTTGAGCAG‑GT‑TGT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGac                                                                                              >  1:1653470/1‑150 (MQ=255)
                                   ctcctTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGacac                                                                                            <  1:758263/150‑1 (MQ=255)
                                       ttGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GCTTCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGtcc                                                                                        >  1:1372970/1‑150 (MQ=255)
                                        tGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGtcct                                                                                       <  2:1108972/150‑1 (MQ=255)
                                            ggTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTg                                                                                   >  1:889182/1‑150 (MQ=255)
                                            ggTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTg                                                                                   >  1:1377235/1‑150 (MQ=255)
                                              tCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GC‑TTC‑TGCGACTTGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCa                                                                                 >  2:970391/1‑150 (MQ=255)
                                                 tAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAgcg                                                                              >  2:110055/1‑150 (MQ=255)
                                                     gtgCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTc                                                                          <  2:517433/150‑1 (MQ=255)
                                                      tgCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAg                                                                                <  2:1091908/143‑1 (MQ=255)
                                                      tgCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GC‑TTC‑TGCGACTTGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAg                                                                                >  1:1091908/1‑143 (MQ=255)
                                                           caCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GC‑TTCTGCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCtt                                                                    >  1:1446755/1‑150 (MQ=255)
                                                            aCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTg                                                                   <  1:970391/150‑1 (MQ=255)
                                                            aCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTg                                                                   <  1:453372/150‑1 (MQ=255)
                                                              ggAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGc                                                                 <  2:362690/150‑1 (MQ=255)
                                                                 aTCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGa                                                                                               <  1:1019456/117‑1 (MQ=255)
                                                                 aTCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GC‑TTC‑TGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGa                                                                                               >  2:1019456/1‑117 (MQ=255)
                                                                      gcggcgTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAgcggcg                                                         >  1:241799/1‑150 (MQ=255)
                                                                                cGGCCATGGCTGATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCAc                                               <  1:187952/150‑1 (MQ=255)
                                                                                        gCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCATGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCacac                                       >  1:1665634/1‑150 (MQ=255)
                                                                                               gAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATa                                <  2:986003/150‑1 (MQ=255)
                                                                                                  cTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGc                             >  2:188356/1‑150 (MQ=255)
                                                                                                     ggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATc                                                 <  2:1420196/127‑1 (MQ=255)
                                                                                                     ggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATc                                                 >  1:1420196/1‑127 (MQ=255)
                                                                                                     ggTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCtt                          <  2:241799/150‑1 (MQ=255)
                                                                                                        ataGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GC‑TTCTGCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTa                       >  2:1605814/1‑150 (MQ=255)
                                                                                                           ggTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt                    <  1:1605814/150‑1 (MQ=255)
                                                                                                             tCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTgg                  >  2:1594388/1‑150 (MQ=255)
                                                                                                                aGCTCTGGTCACCTTCGTGCTTGAG‑CAGCT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAcc               >  2:1272648/1‑150 (MQ=255)
                                                                                                                  ctctGGTCACCTTCGTGCTTGAG‑CAGCT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCg             <  1:944045/150‑1 (MQ=255)
                                                                                                                     tGGTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGcc          >  1:1085234/1‑150 (MQ=255)
                                                                                                                       gTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTAc                      <  2:1015208/136‑1 (MQ=255)
                                                                                                                       gTCACCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTAc                      >  1:1015208/1‑136 (MQ=255)
                                                                                                                          aCCTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGcc                                                                            <  1:1647026/79‑1 (MQ=255)
                                                                                                                          aCCTTCGTGCTTGAG‑CA‑GC‑TTC‑TGCGACTTGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGcc                                                                            >  2:1647026/1‑79 (MQ=255)
                                                                                                                            cTTCGTGCTTGAGCAG‑CT‑TCT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGcc                            >  1:1078984/1‑125 (MQ=255)
                                                                                                                            cTTCGTGCTTGAG‑CA‑GC‑TTC‑TGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCAc   <  2:1377235/150‑1 (MQ=255)
                                                                                                                             ttCGTGCTTGAG‑CA‑GC‑TTC‑TGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACt  >  1:465452/1‑150 (MQ=255)
                                                                                                                                                  |                                                                                                                                     
TCTTCTTTCAGGTTACGGGTCAGGCTGCCATCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AA‑CC‑TCC‑GCCAAC‑TGCATTCGTGAA‑CCAAGCAACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCACT  >  NC_002947/4741137‑4741410

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ 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