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
A14 F1 I1 R1 770 68.5 3470224 91.7% 3182195 103.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,022,810 C→T A65A (GCC→GCT)  fliQ → flagellar biosynthesis protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,022,8100CT97.9% 149.1 / ‑4.1 48A65A (GCC→GCT) fliQflagellar biosynthesis protein
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (24/23);  total (25/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01

GGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAGCCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCT  >  NC_000913/2022702‑2022944
                                                                                                            |                                                                                                                                      
ggTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGAt                                                                                                          <  1:266228/139‑1 (MQ=255)
  tCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTa                                                                                                        >  2:378335/1‑139 (MQ=255)
      gggCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTc                                                                                                    >  2:1631628/1‑139 (MQ=255)
         ccTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGc                                                                                                 <  2:1505810/139‑1 (MQ=255)
           ttATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCAc                                                                                               >  1:248602/1‑139 (MQ=255)
            tATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCAcc                                                                                              <  2:303871/139‑1 (MQ=255)
                   aGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCa                                                                                       >  2:1106157/1‑139 (MQ=255)
                          tGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGa                                                                                                                              <  1:1690416/93‑1 (MQ=255)
                          tGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGa                                                                                                                              >  2:1690416/1‑93 (MQ=255)
                           gCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTg                                                                               <  2:248602/139‑1 (MQ=255)
                            cAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGa                                                                                                                              <  1:310624/91‑1 (MQ=255)
                            cAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGa                                                                                                                              >  2:310624/1‑91 (MQ=255)
                               gccgccACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGa                                                                                                                              >  1:71602/1‑88 (MQ=255)
                               gccgccACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGa                                                                                                                              <  2:71602/88‑1 (MQ=255)
                               gccgccACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTTCTGGATTACGTCCGCa                                                                                                <  1:1077557/118‑1 (MQ=255)
                               gccgccACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGc                                                                                                               <  1:288477/103‑1 (MQ=255)
                               gccgccACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGc                                                                                                               >  2:288477/1‑103 (MQ=255)
                               gccgccACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCa                                                                                                >  2:1077557/1‑118 (MQ=255)
                                 cgccACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGtt                                                                                                                 <  2:292613/99‑1 (MQ=255)
                                 cgccACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGtt                                                                                                                 >  1:292613/1‑99 (MQ=255)
                                   ccACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTatat                                                                       >  2:687143/1‑139 (MQ=255)
                                          gATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCgga                                                                <  1:378335/139‑2 (MQ=255)
                                           aTTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAAc                                                                                  <  2:761968/120‑1 (MQ=255)
                                           aTTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAAc                                                                                  >  1:761968/1‑120 (MQ=255)
                                                cGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCg                                                          <  1:57533/139‑1 (MQ=255)
                                                     tGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGAt                                                                                                          <  2:1321405/86‑1 (MQ=255)
                                                     tGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGAt                                                                                                          >  1:1321405/1‑86 (MQ=255)
                                                       aCGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATg                                                   >  2:1136044/1‑139 (MQ=255)
                                                                       cGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGc                                                                                                 >  2:855334/1‑77 (MQ=255)
                                                                       cGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGc                                                                                                 <  1:855334/77‑1 (MQ=255)
                                                                       cGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTaa                                                             >  2:440577/1‑112 (MQ=255)
                                                                       cGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTaa                                                             <  1:440577/113‑2 (MQ=255)
                                                                       cGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCg                                   >  1:660769/1‑139 (MQ=255)
                                                                       cGAAAATCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCg                                   >  1:657495/1‑139 (MQ=255)
                                                                         aaaaTCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTgg                                                                                                                               >  1:1236071/1‑45 (MQ=255)
                                                                         aaaaTCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTgg                                                                                                                               <  2:1236071/45‑1 (MQ=255)
                                                                         aaaaTCATCGCCGTATTTATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGaa                                 >  1:1335836/1‑139 (MQ=255)
                                                                                         ttATCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGt                 <  1:1631628/139‑1 (MQ=255)
                                                                                            tCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAAc                                <  1:714823/121‑1 (MQ=255)
                                                                                            tCGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAAc                                >  2:714823/1‑121 (MQ=255)
                                                                                             cGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTatat                                                                       <  2:829068/81‑1 (MQ=255)
                                                                                             cGCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTatat                                                                       >  1:829068/1‑81 (MQ=255)
                                                                                              gCCATTATTATTGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAAc            >  1:1703253/1‑139 (MQ=255)
                                                                                                   tattattGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTg                                                >  1:442754/1‑98 (MQ=255)
                                                                                                   tattattGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTg                                                <  2:442754/98‑1 (MQ=255)
                                                                                                        ttGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAg                                     >  1:457331/1‑104 (MQ=255)
                                                                                                        ttGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAg                                     <  2:457331/104‑1 (MQ=255)
                                                                                                        ttGCTGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAACCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCt  <  1:687143/139‑1 (MQ=255)
                                                                                                            |                                                                                                                                      
GGTCACGGGCCTTATCATCAGTATTTTGCAGGCCGCCACGCAGATTAACGAAATGACGCTGTCGTTTATTCCGAAAATCATCGCCGTATTTATCGCCATTATTATTGCCGGACCGTGGATGCTCAATCTGTTGCTGGATTACGTCCGCACCTTGTTCACTAACCTGCCGTATATCATCGGGTAGCCGTACTATGTTGCAGGTGACAAGCGAACAATGGCTATCCTGGTTAAACCTGTACTTCT  >  NC_000913/2022702‑2022944

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A