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 F1 I1 R1 759 65.2 3386260 90.7% 3071337 101.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,266,127 C→T *313* (TAG→TAA)  tdcA ← tdc operon transcriptional activator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,266,1270CT92.9% 73.6 / ‑1.1 28*313* (TAG→TAA) tdcAtdc operon transcriptional activator
Reads supporting (aligned to +/- strand):  ref base C (1/1);  new base T (13/13);  total (14/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.72e-01

ATCAATAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCCA  >  NC_000913/3265993‑3266257
                                                                                                                                      |                                                                                                                                  
atcaATAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAAtaattaac                                                                                                                                >  2:846578/1‑139 (MQ=255)
                             tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCt                                                                                                             >  2:352411/1‑129 (MQ=255)
                             tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCt                                                                                                             <  1:352411/129‑1 (MQ=255)
                             tatGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                   <  1:71804/139‑1 (MQ=255)
                                gCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCt                                                                                                       <  1:1247583/132‑1 (MQ=255)
                                gCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCt                                                                                                       >  2:1247583/1‑132 (MQ=255)
                                    tataAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATtat                                                                                            <  1:846578/139‑1 (MQ=255)
                                           ccTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                              <  2:1646394/114‑1 (MQ=255)
                                           ccTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                              >  1:1646394/1‑114 (MQ=255)
                                           ccTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGa                                                                                     >  2:189501/1‑139 (MQ=255)
                                                tCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCtt                                                                                                            >  2:1436264/1‑111 (MQ=255)
                                                tCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCtt                                                                                                            <  1:1436264/111‑1 (MQ=255)
                                                                  tAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                              <  1:1677017/91‑1 (MQ=255)
                                                                  tAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGcc                                                                                                              >  2:1677017/1‑91 (MQ=255)
                                                                   aGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAAtaattaac                                                                                                                                <  2:132624/72‑1 (MQ=255)
                                                                   aGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAAtaattaac                                                                                                                                >  1:132624/1‑72 (MQ=255)
                                                                      taaccgtaaccgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAAc                                                          >  1:1548828/1‑139 (MQ=255)
                                                                              accgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                   <  1:480668/90‑1 (MQ=255)
                                                                              accgACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTacac                                                                                                   >  2:480668/1‑90 (MQ=255)
                                                                                   cacCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCtttt                                             >  1:649290/1‑139 (MQ=255)
                                                                                         cAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGaa                                                                                    <  1:594950/94‑1 (MQ=255)
                                                                                         cAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGaa                                                                                    >  2:594950/1‑94 (MQ=255)
                                                                                         cAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATa                                       <  2:1548828/139‑1 (MQ=255)
                                                                                                   agGTGGATTATTTATGTTTAAATAAAAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAAtttt                             >  2:394514/1‑139 (MQ=255)
                                                                                                                     taaataaaAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGCTGCTGATTTTTTAATACGATAATTTTTCGACCATACCGCGGCa            <  1:1133219/138‑1 (MQ=255)
                                                                                                                     taaataaaAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCa            >  2:1133219/1‑138 (MQ=255)
                                                                                                                       aataaaAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGaa                                                                                    >  2:103171/1‑64 (MQ=255)
                                                                                                                       aataaaAACAAATAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGaa                                                                                    <  1:103171/64‑1 (MQ=255)
                                                                                                                              aCAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCca  <  1:189501/139‑1 (MQ=255)
                                                                                                                                  aTAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCtt                                                                             <  1:1439366/60‑1 (MQ=255)
                                                                                                                                  aTAATTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCtt                                                                             >  2:1439366/1‑60 (MQ=255)
                                                                                                                                      |                                                                                                                                  
ATCAATAGCAACCGGCAGATCGTATGTAATATGCATTATAAAACCTCTTCGCCTGAATTAAATATGTAGGTAACCGTAACCGACACCTGCAAGACAGACAGGTGGATTATTTATGTTTAAATAAAAACAAATAACTAACCAACTTCTATTAATTGCCTTCGTCTACACCCATTATAAGATGAATACTCTTTGGCTAATTCCACCAAAACCGATGCTGCTTTTTTAATACGATAATTTTTCGACCATACCGCGGCATATTGTGCCA  >  NC_000913/3265993‑3266257

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A