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 I2 R1 765 46.1 2269152 93.8% 2128464 105.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,380,807 G→A *220* (TAG→TAA)  ycjU → beta‑phosphoglucomutase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,380,8070GA100.0% 73.7 / NA 24*220* (TAG→TAA) ycjUbeta‑phosphoglucomutase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (13/11);  total (13/11)

GCGGTATGCGCTCGGTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAGCAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATAAAGAGTTCATCGTGTTTGTCGGCCCGTCGGGCT  >  NC_000913/1380695‑1380941
                                                                                                                |                                                                                                                                      
gCGGTATGCGCTCGGTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCttt                                                                                                              <  1:256479/139‑1 (MQ=255)
 cGGTATGCGCTCGGTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTc                                                                                                             >  1:814025/1‑139 (MQ=255)
   gTATGCGCTCGGTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGt                                                                                                           <  1:129671/139‑1 (MQ=255)
                                   aCCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCAGCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCaaa                                                                                            >  1:692076/1‑122 (MQ=255)
                                   aCCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCaaa                                                                                            <  2:692076/122‑1 (MQ=255)
                                        ggCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCttt                                                                                                              >  1:139062/1‑99 (MQ=255)
                                        ggCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCttt                                                                                                              <  2:139062/99‑1 (MQ=255)
                                        ggCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCt                                                                                                                >  1:170207/1‑97 (MQ=255)
                                        ggCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCt                                                                                                                <  2:170207/97‑1 (MQ=255)
                                                     ttGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCt                                                                                                                <  1:869315/84‑1 (MQ=255)
                                                     ttGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCt                                                                                                                >  2:869315/1‑84 (MQ=255)
                                                               cGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTgg                                               >  2:734836/1‑139 (MQ=255)
                                                                       ctcacCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACTAAGGAATAAACATGGCt                                                                                                                     >  2:60711/1‑61 (MQ=255)
                                                                       ctcacCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCt                                                                                                                     <  1:60711/61‑1 (MQ=255)
                                                                       ctcacCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACg                                                                                   >  1:418275/1‑95 (MQ=255)
                                                                       ctcacCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACg                                                                                   <  2:418275/95‑1 (MQ=255)
                                                                               gCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCtt                                                                                                               >  1:1092681/1‑59 (MQ=255)
                                                                               gCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCtt                                                                                                               <  2:1092681/59‑1 (MQ=255)
                                                                               gCCGCGGTTATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATAAaga                               >  2:760396/1‑139 (MQ=255)
                                                                                      ttATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATaa                                  <  2:164291/129‑1 (MQ=255)
                                                                                      ttATCGGCCTTCTGGCAAAACGTATAACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATaa                                  >  1:164291/1‑129 (MQ=255)
                                                                                                tccggCAAAACGTATAACAAAGGAATCAACATGGCTCAGCt                                                                                                                <  2:959232/38‑1 (MQ=255)
                                                                                                tccggCAAAACGTATAACAAAGGAATCAACATGGCTCAGCt                                                                                                                >  1:959232/4‑41 (MQ=255)
                                                                                                            tataACAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATAAAGAGTTCATCGTGTTTGTCGGCCCGTCGGGCt  >  2:1022567/1‑139 (MQ=255)
                                                                                                                |                                                                                                                                      
GCGGTATGCGCTCGGTGGGGATCGGCGCGGGCTTAACCGGGGCGCAATTACTGTTGCCTTCAACGGAATCACTCACCTGGCCGCGGTTATCGGCCTTCTGGCAAAACGTATAGCAAAGGAATCAACATGGCTCAGCTTTCGTTACAACATATTCAAAAAATCTACGATAACCAGGTGCATGTGGTGAAGGACTTCAACCTGGAAATTGCCGATAAAGAGTTCATCGTGTTTGTCGGCCCGTCGGGCT  >  NC_000913/1380695‑1380941

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ 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