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 F23 I1 R1 6 89.4 4352318 93.8% 4082474 136.0

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_0029474,741,2800CT85.4% 107.8 / 9.6 48intergenic (+471/+281)gltA/yeiWcitrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand):  ref base C (1/6);  new base T (25/16);  total (26/22)
Fisher's exact test for biased strand distribution p-value = 3.76e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.37e-01

GGGTCAGGCTGCCATCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AA‑CCT‑CC‑GCCAAC‑TGCATTCGTGAA‑CCAAGCAACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCAC  >  NC_002947/4741153‑4741409
                                                                                                                                  |                                                                                                                                    
gggTCAGGCTGCCATCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGaatcc                                                                                                               <  2:1888757/150‑4 (MQ=255)
            cATCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGccc                                                                                                  >  2:1267122/1‑150 (MQ=255)
              tCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATCGCGTCTTGACCTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCg                                                                                                <  2:410737/150‑1 (MQ=255)
                          aTGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGCGAATCCAGGC‑ACAGGCCCCGGACACGtcctcc                                                                                    <  2:1135262/150‑1 (MQ=255)
                            ggTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTg                                                                                  >  2:2169701/1‑150 (MQ=255)
                                gTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAAGTGGGTATAGGTCCAGCTCTGGTCAACTGCATGGCTACG‑CG‑GCTGCT‑GCGACT‑TGGACTCGTGAA‑TTCAGGCACATGCCCCGGACACGTCCTCCTGCAgc                                                                              >  1:1458798/1‑150 (MQ=255)
                                gTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GCT‑TC‑TGCGACTTGCATTCGTGaatccag                                                                                                             <  1:1594144/120‑6 (MQ=255)
                                     gtgCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTc                                                                         <  2:1118013/150‑1 (MQ=255)
                                     gtgCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTc                                                                         <  2:2022423/150‑1 (MQ=255)
                                        cagcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGAc                                                                      >  1:1872140/1‑150 (MQ=255)
                                        cagcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACAAGTCCTCCTGCAGCGCCTCGAc                                                                      >  1:1528850/1‑150 (MQ=255)
                                         agcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGtcc                                                                                       >  2:1694980/1‑132 (MQ=255)
                                         agcaCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GCT‑TCTGCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGtcc                                                                                       <  1:1694980/132‑1 (MQ=255)
                                            aCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTg                                                                  <  2:818034/150‑1 (MQ=255)
                                            aCGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GCT‑TC‑TGCGACTTGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTg                                                                  <  2:415355/150‑1 (MQ=255)
                                                     cgcgGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GCT‑TC‑TGCGACTTGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAgcggc                                                         <  2:549024/150‑1 (MQ=255)
                                                            tCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGa                                                  >  2:703402/1‑150 (MQ=255)
                                                             cACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGAt                                                 >  2:1890/1‑150 (MQ=255)
                                                              aCCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATc                                                >  1:994072/1‑150 (MQ=255)
                                                                  gCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CAGCTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACgg                                            <  1:1442284/150‑1 (MQ=255)
                                                                  gCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑CA‑GCT‑TCTGCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACgg                                            <  1:87184/150‑1 (MQ=255)
                                                                   ccATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCGCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGt                                           >  1:782278/1‑150 (MQ=255)
                                                                      tGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCACCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTcac                                        >  1:1718031/1‑150 (MQ=255)
                                                                       ggCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTcaca                                       <  1:12429/150‑1 (MQ=255)
                                                                           taatGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACcgc                                   >  1:2171913/4‑150 (MQ=255)
                                                                               gAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATa                               <  1:717123/150‑1 (MQ=255)
                                                                                      gTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCACCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCtta                        >  1:477207/1‑149 (MQ=255)
                                                                                        ataGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGc                                                                >  1:1503846/1‑108 (MQ=255)
                                                                                        ataGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGc                                                                <  2:1503846/108‑1 (MQ=255)
                                                                                        ataGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTa                      >  1:1354574/1‑150 (MQ=255)
                                                                                         taGGTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTAc                     <  2:1354574/150‑1 (MQ=255)
                                                                                           ggTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACtt                   <  1:2115863/150‑1 (MQ=255)
                                                                                            gTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGacac                                                                                           >  2:2039594/1‑77 (MQ=255)
                                                                                            gTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTg                  >  1:947563/1‑150 (MQ=255)
                                                                                            gTCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGacac                                                                                           <  1:2039594/77‑1 (MQ=255)
                                                                                             tCCAGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTgg                 >  2:1849624/1‑150 (MQ=255)
                                                                                                aGCTCTGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGAcc              >  2:1103648/1‑150 (MQ=255)
                                                                                                    ctGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTc                                                                         <  2:359428/87‑1 (MQ=255)
                                                                                                    ctGGTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTc                                                                         >  1:359428/1‑87 (MQ=255)
                                                                                                       gTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCtt                                                    >  1:1942541/1‑105 (MQ=255)
                                                                                                       gTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAg                              >  2:728671/1‑127 (MQ=255)
                                                                                                       gTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGccgc       >  1:1524314/1‑148 (MQ=255)
                                                                                                       gTCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCtt                                                    <  2:1942541/105‑1 (MQ=255)
                                                                                                       gTCACCTTCGTGCTTGAG‑CA‑GCT‑TC‑TGCGACTTGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAg                              <  1:728671/127‑1 (MQ=255)
                                                                                                        tCACCTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCAcc      >  2:413973/1‑150 (MQ=255)
                                                                                                         cACCTTCGTGCTTGAG‑CAGCTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCt     <  2:1955190/150‑1 (MQ=255)
                                                                                                            cTTCGTGCTTGAGCAG‑CTT‑CT‑GCGACT‑TGCATTCGTGAA‑TCCAGGCACAGGACCCGGAAACGTCGTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATAACGGTGACACGGCGATAGGACTTGTAGTTGGAGACGGAAACCTCAc  >  2:1419327/1‑150 (MQ=255)
                                                                                                            cTTCGTGCTTGAG‑CA‑GCT‑TC‑TGCGACTTGCATTCGTGAATCCAGGC‑ACAGGCCCCGGACACGTCCTCCTACAgcgc                                                                            >  1:438768/1‑76 (MQ=255)
                                                                                                                                  |                                                                                                                                    
GGGTCAGGCTGCCATCCGCCTCCTTGATGGTCGTAATGTGCAGCACGGAATCACGCGGCGTCACCGGCCATGGCGTATTGAACTGGGTATAGGTCCAGCTCTGGTCACCTTCGTGCTTGAG‑AA‑CCT‑CC‑GCCAAC‑TGCATTCGTGAA‑CCAAGCAACAGGCCCCGGACACGTCCTCCTGCAGCGCCTCGACCTTGGCCAGCGGCGCCTTGATCACGGTCACACCGCGATAGGCCTTGTACTTGGACCCGGCCACCTCAC  >  NC_002947/4741153‑4741409

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