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
A7 F1 I1 R1 83 73.5 3575638 92.3% 3300313 107.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,207,900 C→T intergenic (‑368/‑247) purH ← / → rrsE IMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase/16S ribosomal RNA of rrnE operon

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,207,9000CT98.1% 166.9 / ‑6.6 53intergenic (‑368/‑247)purH/rrsEIMP cyclohydrolase and phosphoribosylaminoimidazolecarboxamide formyltransferase/16S ribosomal RNA of rrnE operon
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (28/24);  minor base A (0/1);  total (28/25)
Fisher's exact test for biased strand distribution p-value = 4.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGGTATAAAGCGGGCTTTTGCTGGGGAATGCAGCAGTCAGTCATTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGCCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACAATTTATCAGACAATCTGTGT  >  NC_000913/4207765‑4208034
                                                                                                                                       |                                                                                                                                      
aGGTATAAAGCGGGCTTTTGCTGGGGAATGCAGCAGTCAGTCATTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTcgg                                                                                                                                     <  1:942162/139‑1 (MQ=255)
  gTATAAAGCGGGCTTTTGCTGGGGAATGCAGCAGTCAGTCATTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTcggtt                                                                                                                                   <  2:1756981/139‑1 (MQ=255)
            ggCTTTTGCTGGGGAATGCAGCAGTCAGTCATTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAaga                                                                                                                         >  1:1368257/1‑139 (MQ=255)
                  tGCTGGGGAATGCAGCAGTCAGTCATTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGaaaaa                                                                                                                   <  1:115634/139‑1 (MQ=255)
                            tGCAGCAGTCAGTCATTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGaa                                                                                                                           <  1:1250441/121‑1 (MQ=255)
                            tGCAGCAGTCAGTCATTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGaa                                                                                                                           >  2:1250441/1‑121 (MQ=255)
                                   gtcagtcaTTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTcggtt                                                                                                                                   >  1:1247915/1‑106 (MQ=255)
                                   gtcagtcaTTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTcggtt                                                                                                                                   <  2:1247915/106‑1 (MQ=255)
                                    tcagtcaTTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTg                                                                                                 >  2:1382745/1‑139 (MQ=255)
                                      agtcaTTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGAc                                                                                               <  1:335239/139‑1 (MQ=255)
                                        tcaTTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGActc                                                                                             >  1:153751/1‑139 (MQ=255)
                                                  gCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGa                                                                                   <  1:1486259/139‑1 (MQ=255)
                                                  gCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGa                                                                                   >  2:801467/1‑139 (MQ=255)
                                                       ttttCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCg                                                                              <  2:670614/139‑1 (MQ=255)
                                                                 cGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGc                                                                    <  2:400077/139‑1 (MQ=255)
                                                                 cGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACATCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGc                                                                    <  1:1736114/139‑1 (MQ=255)
                                                                           agaACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGa                                                                                   >  2:30091/1‑114 (MQ=17)
                                                                           agaACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGa                                                                                   <  1:30091/114‑1 (MQ=17)
                                                                           agaACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGa                                                          <  2:153751/139‑1 (MQ=17)
                                                                           agaACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGa                                                          <  1:730520/139‑1 (MQ=17)
                                                                             aaCTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACa                                                        <  1:1382745/139‑1 (MQ=11)
                                                                             aaCTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACGTCACACAAACAGACGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGTGAAGCGTAATATACGCCACCTCGCGACa                                                        <  1:783568/139‑1 (MQ=2)
                                                                                  ccTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTgcg                                                   >  2:973109/1‑139 (MQ=14)
                                                                                  ccTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTgcg                                                   >  2:321207/1‑139 (MQ=14)
                                                                                  ccTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTgcg                                                   >  1:674585/1‑139 (MQ=14)
                                                                                  ccTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTgcg                                                   >  1:1529653/1‑139 (MQ=14)
                                                                                         tGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAgc                                            >  1:655383/1‑139 (MQ=37)
                                                                                         tGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAg                                             >  2:448085/1‑138 (MQ=25)
                                                                                         tGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAg                                             <  1:448085/138‑1 (MQ=37)
                                                                                          gcgcCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAgcg                                           >  1:1350729/1‑139 (MQ=37)
                                                                                          gcgcCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAgcg                                           <  2:1368257/139‑1 (MQ=38)
                                                                                            gcCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGcgcg                                         >  1:480804/1‑139 (MQ=255)
                                                                                            gcCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTAGCGACAGTGCGCTAAAGcgcg                                         >  2:1050093/1‑139 (MQ=255)
                                                                                             ccTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGt                                        >  1:1710091/1‑139 (MQ=255)
                                                                                              cTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTc                                       >  1:111362/1‑139 (MQ=255)
                                                                                                           gcggATGTGAATCACTTCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCttt                          <  2:1529653/139‑1 (MQ=255)
                                                                                                                          ttCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAg                                             >  2:80200/1‑105 (MQ=255)
                                                                                                                          ttCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAg                                             <  1:80200/105‑1 (MQ=255)
                                                                                                                          ttCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACa                      >  1:200268/1‑128 (MQ=255)
                                                                                                                          ttCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACa                      <  2:200268/128‑1 (MQ=255)
                                                                                                                          ttCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACAATTTATCAGAc           >  2:409089/1‑139 (MQ=255)
                                                                                                                          ttCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACAATTTATCAGAc           >  1:926002/1‑139 (MQ=255)
                                                                                                                           tCACACAAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACAATTTATCAGACa          <  2:111362/139‑1 (MQ=255)
                                                                                                                            cacacaAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACAATTTATCAGACa          >  2:283596/1‑138 (MQ=255)
                                                                                                                            cacacaAACAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCGTTAACAATTTATCAGACa          <  1:283596/138‑1 (MQ=255)
                                                                                                                                 aaaCAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGct                              >  2:1638528/1‑113 (MQ=255)
                                                                                                                                 aaaCAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGct                              <  1:1638528/113‑1 (MQ=255)
                                                                                                                                 aaaCAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACAATTTATCAGACAATCtgt    >  2:555968/1‑139 (MQ=255)
                                                                                                                                  aaCAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACAATTTATCAGACa          <  2:1275037/132‑1 (MQ=255)
                                                                                                                                  aaCAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACAATTTATCAGACa          >  1:1275037/1‑132 (MQ=255)
                                                                                                                                   aCAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACAATTTATCAGACAATCtgtgt  >  2:1721664/1‑139 (MQ=255)
                                                                                                                                    cAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACa                      >  2:828144/1‑118 (MQ=255)
                                                                                                                                    cAGTCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACa                      <  1:828144/118‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                      
AGGTATAAAGCGGGCTTTTGCTGGGGAATGCAGCAGTCAGTCATTTTTCTGCAATTTTTCTATTGCGGCCTGCGGAGAACTCCCTATAATGCGCCTCCATCGACACGGCGGATGTGAATCACTTCACACAAACAGCCGGTTCGGTTGAAGAGAAAAATCCTGAAATTCAGGGTTGACTCTGAAAGAGGAAAGCGTAATATACGCCACCTCGCGACAGTGCGCTAAAGCGCGTCGCAACTGCTCTTTAACAATTTATCAGACAATCTGTGT  >  NC_000913/4207765‑4208034

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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