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
A13 F1 I1 R1 778 68.7 3228504 93.4% 3015422 109.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,286,793 A→G intergenic (+267/+273) narI → / ← rttR nitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,286,7930AG92.0% 47.5 / ‑1.8 25intergenic (+267/+273)narI/rttRnitrate reductase 1, gamma (cytochrome b(NR)) subunit/rtT sRNA, processed from tyrT transcript
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base G (10/13);  total (11/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.31e-01

ATCGGGCAAAATTAGCTCGGAGTAACAGGTTTTGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCAAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCTTGGGCA  >  NC_000913/1286659‑1286837
                                                                                                                                        |                                            
aTCGGGCAAAATTAGCTCGGAGTAACAGGTTTTGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTAAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAgcc                                          >  2:987750/1‑137 (MQ=255)
        taattgcggattcgttgggaagttcagggacttttgaaagtGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACctta                                  <  2:932233‑M1/98‑2 (MQ=255)
             gcggattcgttgggaagttcagggacttttgaaagtGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCcgaaccttaatcga                             >  2:636323‑M1/37‑133 (MQ=255)
              gCTCGGAGTAACAGGTTTTGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCttaatcgaa                            <  1:1030154/139‑8 (MQ=17)
              gCTCGGAGTAACAGGTTTTGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGaa                            <  2:398560/139‑1 (MQ=255)
              cggattcgttgggaagttcagggacttttgaaagtGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGaa                            <  2:18997‑M1/104‑1 (MQ=255)
              cggattcgttgggaagttcagggacttttgaaagtGATGGTGGTGGGGG‑‑AAGGATTACTCACCGCTGCGCGCATCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGaa                            <  2:233116‑M1/104‑1 (MQ=255)
                gattcgttgggaagttcagggacttttgaaagtGATGGTGGTGGGGGGGAAGGATTACTCAGCGCTTCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAAc                                      >  2:1287132‑M1/34‑129 (MQ=255)
                gattcgttgggaagttcagggacttttgaaagtGATGGTGGTGGGGGGGAAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGTTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAAc                                      <  1:1287132‑M1/96‑1 (MQ=255)
                   gAGTAACAGGTTTTGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCTtc                       >  1:1337492/1‑139 (MQ=17)
                    aGTAACAGGTTTTGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCTtct                      >  2:1568969/1‑139 (MQ=14)
                      tAACAGGTTTTGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCTTCTCa                    <  1:288992/139‑1 (MQ=14)
                      tAACAGGTTTTGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCTTCTCa                    <  2:555006/139‑1 (MQ=14)
                        aCAGGTTTTGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCTTCTCATc                  >  1:1370808/1‑139 (MQ=14)
                            gTTTTGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AGGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCTTCTCATCCTTc              <  1:1493149/139‑1 (MQ=14)
                              tttGATTATTTCAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCt                         <  2:898354/126‑1 (MQ=14)
                              tttGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCt                         >  1:898354/1‑126 (MQ=14)
                              tttGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCTTCTCATCCTTccc            >  2:166577/1‑139 (MQ=14)
                              tttGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCTTCTCATCCTTccc            >  1:1250198/1‑139 (MQ=255)
                              tttGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCAAGTCGAACCTTGGTCGAAGCTTCTCATCCTTccc            >  2:58454/1‑139 (MQ=255)
                              tttGATTATTTAAGGAAGCGATGGCGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCTTCTCa                    >  1:519775/1‑131 (MQ=14)
                              tttGATTATTTAAGGAAGCGATGGCGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCTTCTCa                    <  2:519775/131‑1 (MQ=14)
                                 gATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCTTCTCATCCTTCCCCGc         <  2:1337492/139‑1 (MQ=11)
                                  attattTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCGAGCCGAACCTTAATCGAAGCTTCTCATCCTTCCCCGca        <  2:520204/139‑2 (MQ=11)
                                        tAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCAAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCTTGGGCa  <  1:58454/139‑1 (MQ=255)
                                                                                                                                        |                                            
ATCGGGCAAAATTAGCTCGGAGTAACAGGTTTTGATTATTTAAGGAAGCGATGGTGGTGGGGG‑‑AAGGATTACTCAGCGCTGCGCGCTTCGCCCTTCGGGTCGTTGCCTGCGGCAACGCTCTCTCGCTGGCGCTCAAGTCGAACCTTGGTCGAAGCTTCTCATCCTTCCCCGCTTGGGCA  >  NC_000913/1286659‑1286837

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