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
A4 F1 I2 R1 780 68.3 3343050 93.5% 3125751 102.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,097,580 (G)7→6 noncoding (73/88 nt) serX ← tRNA‑Ser

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,097,5740G.100.0% 146.0 / NA 38noncoding (79/88 nt)serXtRNA‑Ser
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (24/14);  total (24/14)

CTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACC  >  NC_000913/1097451‑1097706
                                                                                                                           |                                                                                                                                    
cTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAAccc                                                                                                                      >  2:79789/1‑139 (MQ=18)
       aCTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATa                                                                                                                <  2:237736/138‑1 (MQ=255)
       aCTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATa                                                                                                                >  1:237736/1‑138 (MQ=255)
                     gTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGaa                                                                                                                         <  2:881070/115‑1 (MQ=14)
                     gTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGaa                                                                                                                         >  1:881070/1‑115 (MQ=14)
                           gAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAAGCCCCGATACGTTGCCGTATACACACTTTc                                                                                           >  2:1131833/1‑139 (MQ=255)
                                ccGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGc                                                                                      >  2:2551/1‑139 (MQ=255)
                                   gTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTg                                                                                   <  1:2551/139‑1 (MQ=255)
                                   gTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTg                                                                                   <  1:1312993/139‑1 (MQ=255)
                                   gTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTg                                                                                   >  2:1312993/1‑139 (MQ=255)
                                               cATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATaca                                                                                                  >  1:250481/1‑112 (MQ=255)
                                               cATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATaca                                                                                                  <  2:250481/112‑1 (MQ=255)
                                                        ggTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATTGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGa                                                                 >  1:402592/1‑136 (MQ=255)
                                                        ggTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATTGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGa                                                                 <  2:402592/136‑1 (MQ=255)
                                                            tgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACg                                                                                                              <  1:1611661/87‑1 (MQ=255)
                                                            tgtgCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACg                                                                                                              >  2:1611661/1‑87 (MQ=255)
                                                                    ataCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTg                                                                                   <  2:330812/106‑1 (MQ=255)
                                                                    ataCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTg                                                                                   >  1:330812/1‑106 (MQ=255)
                                                                      aCGGAAAAAAAGCCCGTACTGTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATacaca                                                                                                >  2:1133794/1‑91 (MQ=14)
                                                                      aCGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATacaca                                                                                                <  1:1133794/91‑1 (MQ=255)
                                                                             aaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTg                                         >  2:1670707/1‑139 (MQ=255)
                                                                             aaaaGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTg                                         >  1:1363771/1‑139 (MQ=255)
                                                                                              tACGAGCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGgcg                        <  1:1670707/139‑1 (MQ=255)
                                                                                                   gCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGgcg                        >  2:722501/1‑134 (MQ=255)
                                                                                                   gCTCTTCTTTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGgcg                        <  1:722501/134‑1 (MQ=255)
                                                                                                       ttcttTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCATATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAg               >  2:721754/1‑139 (MQ=255)
                                                                                                         cttTAAATATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTAGCTGGAACGGGCGCTAATTTAggg             <  1:1131833/139‑1 (MQ=255)
                                                                                                             aaaTATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTc                                            >  2:87299/1‑104 (MQ=25)
                                                                                                             aaaTATGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTc                                            <  1:87299/104‑1 (MQ=25)
                                                                                                                 atGGCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATg     >  2:1383704/1‑139 (MQ=255)
                                                                                                                   ggCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGAc   >  1:563451/1‑139 (MQ=255)
                                                                                                                   ggCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGAc   >  2:450948/1‑139 (MQ=255)
                                                                                                                   ggCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGAc   >  2:1035140/1‑139 (MQ=255)
                                                                                                                    gCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGgcg                        <  1:1148110/117‑1 (MQ=255)
                                                                                                                    gCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGgcg                        >  2:1148110/1‑117 (MQ=255)
                                                                                                                    gCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGAcc  >  2:1429434/1‑139 (MQ=255)
                                                                                                                    gCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGAcc  >  2:72343/1‑139 (MQ=255)
                                                                                                                    gCGGTGA‑GGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGAcc  >  2:1103197/1‑139 (MQ=255)
                                                                                                                           |                                                                                                                                    
CTGTCCAACTGGCTGTCGCCAGTTGTCGAACCCCGGTCGGGGCTTCTCATCCCCCCGGTGTGTGCAATATACGAAAAAAAAGCCCGTACTTTCGTACGAGCTCTTCTTTAAATATGGCGGTGAGGGGGGGATTCGAACCCCCGATACGTTGCCGTATACACACTTTCCAGGCGTGCTCCTTCAGCCACTCGGACACCTCACCAAATTGTCGTTCCTGTCTTGCTGGAACGGGCGCTAATTTAGGGAAATCATGACC  >  NC_000913/1097451‑1097706

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A