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
A1 F1 I1 R1 66 20.9 912876 97.7% 891879 114.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,490,935 A→G L69L (TTG→CTG)  idnR ← transcriptional repressor, 5‑gluconate‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,490,9350AG100.0% 71.5 / NA 20L69L (TTG→CTG) idnRtranscriptional repressor, 5‑gluconate‑binding
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (9/11);  total (9/11)

ACCGACTCTTCTTCGGAATCGCGATCGTAATTGTAATTAGCAATAAGGGTCTGATAATTATGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAAGATACCGAGGGTATAACTTTGTGCATTCAACAACATGCCGGGAGCGCGATTAGGGATATAATTGATCTCTTCCATAATTTTGGCGATGCGCTCGCCTGTTTCCTTTGCCACCTTTTTCGGCGA  >  NC_000913/4490805‑4491058
                                                                                                                                  |                                                                                                                           
aCCGACTCTTCTTCGGAATCGCGATCGTAATTGTAATTAGCAATAAGGGTCTGATAATTATGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGa                                                                                                                     <  1:120663/139‑1 (MQ=255)
   gACTCTTCTTCGGAATCGCGATCGTAATTGTAATTAGCAATAAGGGTCTGATAATTATGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGa                                                                                                                     <  1:201740/136‑1 (MQ=255)
   gACTCTTCTTCGGAATCGCGATCGTAATTGTAATTAGCAATAAGGGTCTGATAATTATGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGa                                                                                                                     >  2:201740/1‑136 (MQ=255)
   gACTCTTCTTCGGAATCGCGATCGTAATTGTAATTAGCAATAAGGGTCTGATAATTATGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGAggg                                                                                                                  >  1:234737/1‑139 (MQ=255)
               gAATCGCGATCGTAATTGTAATTAGCAATAAGGGTCTGATAATTATGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGAGGGTATAACTTtgtg                                                                                                      <  1:77559/139‑1 (MQ=255)
                  tCGCGATCGTAATTGTAATTAGCAATAAGGGTCTGATAATTATGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGAGGGTATAACTTTGTGCAt                                                                                                   >  1:178740/1‑139 (MQ=255)
                   cgcgATCGTAATTGTAATTAGCAATAAGGGTCTGATAATTATGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGAGGGTATAACTTTGTGCAtt                                                                                                  <  2:234737/139‑1 (MQ=255)
                                    ttAGCAATAAGGGTCTGATAATTATGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGAGGGTATAACTTTGTGCATTCAACAACATGCCGGGAg                                                                                 <  1:11886/139‑1 (MQ=255)
                                                gTCTGATAATTATGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATGTTGAAATGACGGAATCAGGATACCGAGGGTATCACTTTGTGCATTCAACAACATGACGGAAGCGCGCTTAGGGa                                                                     >  2:369722/1‑139 (MQ=255)
                                                  cTGATAATTATGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGAGGGTATAACTTTGTGCATTCAACAACATGCCGGGAGCGCGATTAGGGata                                                                   >  2:15599/1‑139 (MQ=255)
                                                            tGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGAGGGTATAACTTtgtg                                                                                                      >  2:434924/1‑94 (MQ=255)
                                                            tGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGAGGGTATAACTTtgtg                                                                                                      <  1:434924/94‑1 (MQ=255)
                                                                   agGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATCTTGAAATGACGGAATCAGGATACCGAGGGTATAACTTTGTGCATTCAACAACATGCCGGGAGCGCGATTAGGGATATAATTGATCTCTTCCAt                                                  >  1:166223/1‑139 (MQ=255)
                                                                             ttCTACTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGAGGGTATAATTTTGTGCATTCAACAACATGCCGGGAGCGCGATTAGGGATATAATTGATCTCTTCCATAATTTTGGCg                                        <  1:283761/139‑1 (MQ=255)
                                                                                                   gCGAAGAGTTGATTTTGAAATGACGGAATCAGGATACCGAGGGTATAACTTTGTGCATTCAACAACATGCCGGGAGCGCGATTAGGGATATAATTGATCTCTTCCATAATTTTGGCGATGCGCTCGCCTGTTTCCTTTg                  <  1:15599/139‑1 (MQ=255)
                                                                                                                   gAAATGACGGAATCAGGATACCGAGGGTATAACTTTGTGCATTCAACAACATGCCGGGAGCGCGATTAGGGATATAATTGATCTCTTCCATAATTTTGGCGATGCGCTCGCCTGTTTCCTTTGCCACCTTTTTCGGCGa  <  2:178740/139‑1 (MQ=255)
                                                                                                                     aaTGACGGAATCAGGATACCGAGGGTATAACTTTGTGCATTCAACAACATGCCGGGAg                                                                                 <  1:390958/58‑1 (MQ=255)
                                                                                                                     aaTGACGGAATCAGGATACCGAGGGTATAACTTTGTGCATTCAACAACATGCCGGGAg                                                                                 >  2:390958/1‑58 (MQ=255)
                                                                                                                         aCGGAATCAGGATACCGAGGGTATAACTTTGTGCATTCAACAACATGCCGGGAGCGCGATTAg                                                                        <  2:435512/63‑1 (MQ=255)
                                                                                                                         aCGGAATCAGGATACCGAGGGTATAACTTTGTGCATTCAACAACATGCCGGGAGCGCGATTAg                                                                        >  1:435512/1‑63 (MQ=255)
                                                                                                                                  |                                                                                                                           
ACCGACTCTTCTTCGGAATCGCGATCGTAATTGTAATTAGCAATAAGGGTCTGATAATTATGCTCAGAGGTGACGGATTCTATTCCCGCGAGAATGTCAGCGAAGAGTTGATTTTGAAATGACGGAATCAAGATACCGAGGGTATAACTTTGTGCATTCAACAACATGCCGGGAGCGCGATTAGGGATATAATTGATCTCTTCCATAATTTTGGCGATGCGCTCGCCTGTTTCCTTTGCCACCTTTTTCGGCGA  >  NC_000913/4490805‑4491058

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ 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