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
A0 F0 I1 R1 146 27.9 2327082 89.7% 2087392 107.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA AM260479 2,787,923 +C intergenic (+165/‑55) cafA2 → / → moaA1 Ribonuclease G and E/molybdopterin biosynthesis protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*AM2604792,787,9201.C100.0% 45.1 / NA 13intergenic (+162/‑58)cafA2/moaA1Ribonuclease G and E/molybdopterin biosynthesis protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (7/6);  total (7/6)

CCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCG‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGA  >  AM260479/2787799‑2788035
                                                                                                                          |                                                                                                                   
ccACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTgg                                                                                                          >  1:12176/1‑134 (MQ=255)
    gCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCAc                                                                                                      >  1:342540/1‑134 (MQ=255)
              tttttCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCCCGAGCGCCCCTGATTTGGCCACCCCGCCAGGc                                                                                            >  1:528677/1‑134 (MQ=255)
                          aGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGAc                                                                                <  2:342540/134‑1 (MQ=255)
                                    aTGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGccca                                                                      <  2:12176/134‑1 (MQ=255)
                                    aTGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGccca                                                                      <  2:225115/134‑1 (MQ=255)
                                                 aTCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCg                                                                                   <  1:18334/108‑1 (MQ=255)
                                                 aTCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCg                                                                                   >  2:18334/1‑108 (MQ=255)
                                                        ggggATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAAt                                                  >  1:362714/1‑134 (MQ=255)
                                                                       ccACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGAttt                                   <  2:518489/134‑1 (MQ=255)
                                                                                              gcagcaGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTAc            >  1:122862/1‑134 (MQ=255)
                                                                                                        gCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGa  <  1:642134/134‑1 (MQ=255)
                                                                                                        gCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGa  >  2:642134/1‑134 (MQ=255)
                                                                                                                          |                                                                                                                   
CCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCG‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGA  >  AM260479/2787799‑2788035

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

BRESEQ :: bam2aln output
GCAAGAAGGGGACGGCCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCG‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGACGCCCAGCATTCCCGGCAAGCT  >  AM260479/2787784‑2788057
                                                                                                                                            |                                                                                                                                      
GCAAGAAGGGGACGGCCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGC                                                                                                                               >  GWNJ‑0478:712:GW2002102894th:2:1101:14115:80016/1‑150 (MQ=60)
    GAAGGGGACGGCCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCtgt                                                                                                                           >  GWNJ‑0478:712:GW2002102894th:2:1201:9913:39086/1‑147 (MQ=60)
    GAAGGGGACGGCCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCtgt                                                                                                                           >  GWNJ‑0478:712:GW2002102894th:2:2107:4318:55160/1‑147 (MQ=60)
    GAAGGGGACGGCCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACG                                                                                                                           >  GWNJ‑0478:712:GW2002102894th:2:1205:1425:46430/1‑150 (MQ=60)
              GCCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCCCGAGCGCCCCTGATTTGGCCACCCCGCCAGGCC                                                                                                                 >  GWNJ‑0478:712:GW2002102894th:2:1215:7998:41829/1‑150 (MQ=60)
                                      ataagagacagGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACC                                                                                          <  GWNJ‑0478:712:GW2002102894th:2:1103:14389:19367/138‑1 (MQ=60)
                                                        TCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATC                                                                       >  GWNJ‑0478:712:GW2002102894th:2:1204:6289:66572/1‑150 (MQ=60)
                                                                 TCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgt                                                              >  GWNJ‑0478:712:GW2002102894th:2:1115:17254:61748/1‑94 (MQ=60)
                                                                 TCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgt                                                              >  GWNJ‑0478:712:GW2002102894th:2:1203:17542:6103/1‑94 (MQ=60)
                                                                                              GCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACC                                 >  GWNJ‑0478:712:GW2002102894th:2:1108:20449:42631/1‑150 (MQ=60)
                                                                                                                      agatgtgtataagagacagcCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGACGCCCAGCATTCCCG         <  GWNJ‑0478:712:GW2002102894th:2:2216:18587:58273/130‑1 (MQ=60)
                                                                                                                      GGCATCCGGCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGACGCCCAGCATTCCCG         <  GWNJ‑0478:712:GW2002102894th:2:2105:12246:73922/150‑1 (MQ=60)
                                                                                                                              GCCCTCGAGCGCCCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACctgtctcttatacacatctccgagcccacgagacactcgctaatctcgtatgccgtcttctgcttgaaaaaaaaaaaaagcaaaa  >  GWNJ‑0478:712:GW2002102894th:2:1212:12870:72699/1‑64 (MQ=60)
                                                                                                                                            |                                                                                                                                      
GCAAGAAGGGGACGGCCACGCCGTCTCCTTTTTTCATGGGCAGCCGGCCGGATGAATCCCCGCCATCTCCGGGGGATGCGGGTGCCCCACCCCCGCCTCGGCTAGAATGGCAGCAGAAGGCATCCGGCCCTCGAGCG‑CCCTGATTTGGCCACGCCGCCAGGCCGCTCCCCGGACGCCGTGCCCACCCACAGGCCATGACCGAATCCGTCATTCCGATTTTCGACCTGCGCGACCATCGCTACCGCTCGATGACGCCCAGCATTCCCGGCAAGCT  >  AM260479/2787784‑2788057

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 0 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑