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 1,559,680 G→A G77G (GGC→GGT)  ddpC ← D,D‑dipeptide ABC transporter permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,559,6800GA100.0% 59.5 / NA 20G77G (GGC→GGT) ddpCD,D‑dipeptide ABC transporter permease
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (11/9);  total (11/9)

CACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTGCCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCGCCAGCCACGGTGAAAAAATCATCATCAATAGCATTAATACAATGATGACTGCGCTGGTC  >  NC_000913/1559553‑1559809
                                                                                                                               |                                                                                                                                 
cacCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTg                                                                                                                        >  1:650856/1‑139 (MQ=255)
             tCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAggc                                                                                                           >  1:553906/1‑139 (MQ=255)
                        aaCCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAggcg                                                                                                >  1:553849/1‑139 (MQ=255)
                         aCCAATCATACCCGCAATGGCAACCACGACTAAGCCGGCGAGAATTGAGTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCCCTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAggcgg                                                                                               <  2:75196/139‑1 (MQ=255)
                                    ccGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATc                                                                                    >  1:608861/1‑139 (MQ=255)
                                      gCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCaa                                                                                  <  2:245011/139‑1 (MQ=255)
                                                       tAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGc                                                                 >  1:572925/1‑139 (MQ=255)
                                                                  gaATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCgccagcca                                                      <  1:563262/139‑1 (MQ=255)
                                                                   aaTTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGt                                                                                          <  1:221125/102‑1 (MQ=255)
                                                                   aaTTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGt                                                                                          >  2:221125/1‑102 (MQ=255)
                                                                    attgattgCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCGCCAGCCACg                                                    >  1:770674/1‑139 (MQ=255)
                                                                                        cAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCGCCAGCCACGGTGAAAAAATCATCATCAAt                                <  2:553906/139‑1 (MQ=255)
                                                                                          gTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCGCCAGCCACGGTGAAAAAATCATCATCAATAg                              <  1:467172/139‑1 (MQ=255)
                                                                                               cgGCTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCGCCAGCCACGGTGAAAAAATCATCATCAATAGCATTa                         <  2:364096/139‑1 (MQ=255)
                                                                                                  cTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCGCCAGCCACGGTGAAAAAATCATCATCAATAGCATTAATa                      >  2:753679/1‑139 (MQ=255)
                                                                                                  cTAAACAGATCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCGCCAGCCACGGTGAAAAAATCATCATCAATAGCATTAATa                      >  1:548720/1‑139 (MQ=255)
                                                                                                          aTCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCGCCAGCCACGGTGaaaaaa                                           >  1:314790/1‑110 (MQ=255)
                                                                                                          aTCGCGTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCGCCAGCCACGGTGaaaaaa                                           <  2:314790/110‑1 (MQ=255)
                                                                                                               gTCCCACTTCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCACCAGCCACGGTGAAAAAATCATCATCAATAGCATTAATATAATGATGACTgc         <  2:553849/139‑1 (MQ=255)
                                                                                                                      ttCATCGGTACCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCGCCAGCCACGGTGAAAAAATCATCATCAATAGCATTAATACAATGATGACTGCGCTGGTc  >  1:759627/1‑139 (MQ=255)
                                                                                                                               |                                                                                                                                 
CACCGGATAGACATCCGAGTAGCGAACCAATCATACCCGCAATGGCAACCACGACTAATCCGGCGAGAATTGATTGCTGACTGCCGACCAGTACGCGGCTAAACAGATCGCGTCCCACTTCATCGGTGCCAAACCAGTGCGCCGCAGAAGGCGGCAAAAGGCGGGCGGTTAAATCAATGGCGTTGGGATCATGCGTCGCCAGCCACGGTGAAAAAATCATCATCAATAGCATTAATACAATGATGACTGCGCTGGTC  >  NC_000913/1559553‑1559809

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 23 ≤ 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