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 F18 I0 R1 150 105.7 2655328 79.3% 2105675 226.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 766,738 A→G 28.0% E252G (GAG→GGG)  mngA → fused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913766,7380AG28.0% 43.7 / 2.2 27E252G (GAG→GGG) mngAfused 2‑O‑a‑mannosyl‑D‑glycerate specific PTS enzymes: IIA component/IIB component/IIC component
Reads supporting (aligned to +/- strand):  ref base A (12/7);  new base G (4/4);  total (16/11)
Fisher's exact test for biased strand distribution p-value = 6.75e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTCCGGCGGGTATTGCTCACACCTATATGGCTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTAC‑GTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAACGGCGGATC‑AACTCAATAGTGCAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGTACCGTTGATTGTCGCGGGGGGCACGGTGCTGGCGGTCG  >  NC_000913/766557‑766974
                                                                                                                                                                                       |                                                                                                                                                                                                                                            
tGTCCGGCGGGTATTGCTCACACCTATATGGCTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTAC‑GTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAACGGCGGAACAAAACCAAAATTGACACACCCGGTGTTTTTTGGCGTGGAGTGGCGATCAGGGGAGGAGAGGGTTTTAATGGCTTTCCCCCACTTCCCGTCCCCGTTGCGGACCCGAtag                                                                                                                                                                                      >  2:610587/1‑237 (MQ=255)
                         atatGGCTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTAC‑GTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAACGGCGGATC‑AACTCAATAGTGCAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGGGGGGGAGCGGTTTAATGGCATTTCCGCGCTTTCAGGGCCTTTTGCCGAGCCCATTCGCCATGCCGAAGCGTTTTTCcaacaa                                                                                                                                                            >  1:455948/1‑239 (MQ=255)
                               cTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTAC‑GTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAACGGCGGATC‑AACTCAATAGTGCAACCGCCTGTATTTTTTCGGCTGAAGTCGCCATCAAGGGGAGTGAGCGGTTTAATGGCATTCCCCCGCTTTCCAGGCCTGTTTCCGCGCCCGTTCGCCATGCAGAACAGCTTATCCCACAAACGCt                                                                                                                                                       >  1:1193120/1‑238 (MQ=255)
                                 gCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTAC‑GTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAACGGCGGATC‑AACTCAATAGTGCAACCGCCTGTATTTTTTCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGGTTTAATGGCATTCCCGCGCTTTCAATGACTGTTGCCGAGCCCATTCCCCCATCCGAAAGGGTGATCCCACAAGGCCTTa                                                                                                                                                     >  1:1013391/1‑238 (MQ=255)
                                 gCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTAC‑GTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAACGGCGGATC‑AACTCAATAATGCAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATTGCATTCCCGCGCTTTCCGTGCCTGTTGCCGGACCGGTTCCCCATGCCGAAGCGTTTGTCcaacaaaacgttt                                                                                                                                                     >  1:12593/1‑231 (MQ=255)
                                                  aggcgcgccaaaaCTGGGGATAAATGTTTACGGTTAAAAAAAAGGGCGATAGCGGCGTGGAGGGGCTTTGAACGGCGAATA‑AACAAAATGGTACAGCCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGAt                                                                                                                                    <  1:498748/229‑1 (MQ=255)
                                                                                                                                  tctacccAATGGTACAGCCGCCTGTATGTTTGCGGATGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGGGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGa                                                      <  1:1310840/232‑1 (MQ=255)
                                                                                                                                         aaTAGTGCAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCCCTGTTGAGCGGAATCTCttt                                              >  1:196424/1‑239 (MQ=255)
                                                                                                                                         aaTAGTGCAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGCTGATCCAACAATCGCTTACCCTCAAGCGTAGCGATgag                                                                                                                                 >  1:1228012/1‑156 (MQ=255)
                                                                                                                                              tGCAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGGGAGTGAGCGTTTTAATGACATTCCCGCGCTTTCAGCGCCGAGTGCCGAGCCGATTCGCCATGCAGAAGCGGTGACCCAACAAGCGCTTACCCTCAATCGCAGCGATGAGACGCGGACCTTACCACAAGATACCCAACCGGTGAAAAGAGTCAAAACGGGGCTAAAAAAGCAACGGTTGAGCGAACACCCTTTTGcgg                                         >  2:464682/1‑237 (MQ=255)
                                                                                                                                              tGCAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGcc                                          >  1:761601/1‑238 (MQ=255)
                                                                                                                                                cAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCa                                                                                                                <  1:104021/166‑1 (MQ=255)
                                                                                                                                                cAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCa                                                                                                                >  2:104021/1‑166 (MQ=255)
                                                                                                                                                cAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGt                                        >  1:1103676/1‑238 (MQ=255)
                                                                                                                                                cAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGGGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGt                                        >  1:389986/1‑238 (MQ=255)
                                                                                                                                                cAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGGGAAAAGTGTCAAAACGGGGCTGCAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGt                                        >  1:607464/1‑238 (MQ=255)
                                                                                                                                                 aaCCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGtc                                       >  1:167976/1‑237 (MQ=255)
                                                                                                                                                   ccGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGTACCg                                    >  1:326238/1‑239 (MQ=255)
                                                                                                                                                                 ggggtggAAGTCCCAATCGAGGGGAGGGGGCGTTTTAATGGCATTTCCGCGGTTTCAGTGCCTGTTGCCGGGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGTACCGTTGATTGTCGCggg                      <  1:1281785/233‑1 (MQ=255)
                                                                                                                                                                    gCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAAACGCGCACCGTACAGCCAGGTACGCAACCGGTGAAAATTGTAAAACCGGCGGCTAAACAGGCACGTGTAAGGGGAATCCCTTTTGCCGTACCGGTGAATAGAGCgggggg                   >  2:530698/1‑239 (MQ=255)
                                                                                                                                                                       gcatgcgcaagcAAGGAGAGTGACCGTTTTAATGGCATTCCCGCGCTTTCATGGACTGTGGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGTACCGTTGATTGTCGCGGGGGGCa                 <  1:899198/227‑1 (MQ=255)
                                                                                                                                                                       gAAGTCGACATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGTACCGTTGATTGTCGCGGGGGGCa                 <  1:404052/238‑1 (MQ=255)
                                                                                                                                                                                   aaGGGGAGTGGGCGTTTTCAGGGCATTCCCGCGCTTACAGGGCCTGGTGCCGAGCCGATTCGCCATGCAGAAGCGTTTATCCAACAAGCGCTTACCCTAGAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGTACCGTTGAGTGTCGCGGGGGGCACGGTGCTGGCGGt    <  2:326238/239‑1 (MQ=255)
                                                                                                                                                                                   aaGGGGAGTGAGGGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGGGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCTCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGTACCGTTGATTGTCGCGGGGGGCACGGTGCTGGCGGt    <  1:615439/239‑1 (MQ=255)
                                                                                                                                                                                   aaGGGGAGTGAGCGTTTTAATGGCATGCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGTACCGTTGATTGTCGCGGGGGGCACGGTGCTGGCGGt    <  1:1241482/239‑1 (MQ=255)
                                                                                                                                                                                   aaGGAGAGTGAGCGTTTTAATGGCATTCCCGGGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTAAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGTACCGTTGATTGTCGCGGGGGGCACGGTGCTGGCGGt    <  1:428247/239‑1 (MQ=255)
                                                                                                                                                                                    aGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTA‑CCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGTACCGTTGATTGTCGCGGGGGGCACGGTGCTGGCGGTcg  <  1:178231/239‑1 (MQ=255)
                                                                                                                                                                                       |                                                                                                                                                                                                                                            
TGTCCGGCGGGTATTGCTCACACCTATATGGCTGCGGAATATCTGGAAAAAGCCGGACGCAAACTCGGCGTAAATGTTTAC‑GTTGAAAAACAAGGCGCTAACGGCATTGAAGGGCGTTTAACGGCGGATC‑AACTCAATAGTGCAACCGCCTGTATTTTTGCGGCTGAAGTCGCCATCAAGGAGAGTGAGCGTTTTAATGGCATTCCCGCGCTTTCAGTGCCTGTTGCCGAGCCGATTCGCCATGCAGAAGCGTTGATCCAACAAGCGCTTACCCTCAAGCGTAGCGATGAGACGCGTACCGTACAGCAAGATACGCAACCGGTGAAAAGTGTCAAAACGGAGCTGAAACAGGCACTGTTGAGCGGAATCTCTTTTGCCGTACCGTTGATTGTCGCGGGGGGCACGGTGCTGGCGGTCG  >  NC_000913/766557‑766974

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A