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 I2 R1 762 35.5 1545288 95.5% 1475750 117.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,304,813 (C)7→8 coding (1005/1245 nt) mtr ← tryptophan transporter of high affinity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,304,8061.C100.0% 50.7 / NA 16L338V (CTG→GTG) mtrtryptophan transporter of high affinity
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (11/5);  total (11/5)

CCCCAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAAC  >  NC_000913/3304670‑3304931
                                                                                                                                         |                                                                                                                              
ccccAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑cc                                                                                                                             <  2:559075/139‑1 (MQ=255)
ccccAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑cc                                                                                                                             <  2:242361/139‑1 (MQ=255)
   cAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAAGAATCCGTTCGGGAACAACAG‑‑ccccc                                                                                                                          <  1:696591/139‑1 (MQ=255)
                              cGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGCCCCCCCCCACAACTGGCGGGGCAAAGGTCAg                                                                                                 <  1:148856/139‑1 (MQ=255)
                                                   aaCAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACCGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGCGCAAAGGTCAGCAATGCCGTCTTCAAGCGGccc                                                                           >  2:56849/1‑139 (MQ=255)
                                                   aaCAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGccc                                                                           >  1:77370/1‑139 (MQ=255)
                                                          ccGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCg                                                                    >  1:237202/1‑139 (MQ=255)
                                                            ggAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAg                                                                  <  2:355145/139‑1 (MQ=255)
                                                                                  tAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAAAAACAGC‑CCCCCCCACAACTAGCGGGGCAAAGGTCAGAAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTg                                            >  2:220861/1‑139 (MQ=255)
                                                                                                 cATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTcaaaca                             >  1:89403/1‑139 (MQ=255)
                                                                                                     aCCAATGGCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAAcc                         <  2:280609/139‑1 (MQ=255)
                                                                                                           ggCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAg                                                                                                      >  2:25485/1‑56 (MQ=255)
                                                                                                           ggCGTACAGGAATCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAg                                                                                                      <  1:25485/56‑1 (MQ=255)
                                                                                                                      aTCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGga        >  1:668123/1‑139 (MQ=255)
                                                                                                                       tCCGTTCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGgaa       >  2:557706/1‑139 (MQ=255)
                                                                                                                           ttCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGgaacgaa   >  1:268824/1‑139 (MQ=255)
                                                                                                                            tCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAg                                                                                 <  1:307762/60‑1 (MQ=255)
                                                                                                                            tCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAg                                                                                 >  2:307762/1‑60 (MQ=255)
                                                                                                                            tCGGGAACAACAGC‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGgaacgaac  >  1:308344/1‑139 (MQ=255)
                                                                                                                                         |                                                                                                                              
CCCCAGACGCGGAATTTCGGGCTGCCAAAGCGTTTACGCGATGCACGGGCTAACAGCGCCGGAACAATTGCCGCCCAGATGGTAGCCGCTAAACCAGCATAACCAATGGCGTACAGGAATCCGTTCGGGAACAACAG‑‑CCCCCCCACAACTGGCGGGGCAAAGGTCAGCAATGCCGTTTTCAAGCGGCCCACAGCCGAGTCGTCGAAACCAAACAGATCTGCCAGATAGTCAAACAAACCCAGCGTTACGCCGAGGAACGAAC  >  NC_000913/3304670‑3304931

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A