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
A10 F28 I1 R1 126 51.4 1736588 99.0% 1719222 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,622,761 G→C R1190R (CGG→CGC)  rhsB → rhs element protein RhsB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,622,7610GC94.1% 30.7 / ‑2.9 17coding (3570/4236 nt)rhsBrhs element protein RhsB
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base C (5/11);  minor base . (0/1);  total (5/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

TGATGAATGGGGCAACCTGCTGAATGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGGCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAACCTGTA  >  NC_000913/3622701‑3622886
                                                            |                                                                                                                             
cgatgaATGGGGCAACCTGCTGAATGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCC‑‑‑‑GCCGGGGCAGCAGTACGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGatatat                                            <  2:762707/139‑1 (MQ=11)
                                aCCCGCATCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAgggg                >  2:533893/1‑140 (MQ=14)
                                 cccGCATCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAggggg               >  1:436716/1‑140 (MQ=14)
                                   cGCATCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGa             <  1:37549/140‑1 (MQ=18)
                                   cGCATCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGa             <  2:325058/140‑1 (MQ=18)
                                    gCATCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGAt            >  1:147616/1‑140 (MQ=14)
                                     cATCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATg           >  2:261906/1‑140 (MQ=14)
                                      aTCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATgg          <  2:147616/140‑1 (MQ=17)
                                       tCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGa         <  1:31386/140‑1 (MQ=18)
                                       tCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGa         <  2:588037/140‑1 (MQ=18)
                                       tCAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGa         <  2:549573/140‑1 (MQ=17)
                                        cAGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGaa        <  1:365775/140‑1 (MQ=18)
                                         aGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAAc       <  2:449359/140‑1 (MQ=18)
                                         aGCTGCAGCAGCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACCCAGGATCCGATTGGACTGAAGGGGGGATGGAAc       <  2:202769/140‑1 (MQ=19)
                                              cagcagCTTATCCGCCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAACCTGTa  <  2:682636/140‑1 (MQ=255)
                                                    cTTATCCGCCTGCCGTGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGa             >  1:796113/1‑123 (MQ=9)
                                                    cTTATCCGCCTGCCGTGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGa             <  2:796113/123‑1 (MQ=17)
                                                            |                                                                                                                             
TGATGAATGGGGCAACCTGCTGAATGAAGAGAACCCGCATCAGCTGCAGCAGCTTATCCGGCTGCCGGGGCAGCAGTATGATGAGGAGTCCGGCCTGTATTACAACCGCCACCGCTATTATGACCCGCTGCAGGGGCGATATATCACTCAGGATCCGATTGGACTGAAGGGGGGATGGAACCTGTA  >  NC_000913/3622701‑3622886

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A