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
A2 F5 I179 R1	182	40.3	1547118	96.8%	1497610	120.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	966,040	A→G	D399G (GAT→GGT)	ycaQ →	winged helix DNA‑binding protein YcaQ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	966,040	0	A	G	100.0%	111.4 / NA	29	D399G (GAT→GGT)	ycaQ	winged helix DNA‑binding protein YcaQ
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (17/12); total (17/12)

GTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTG  >  NZ_CP009273/965912‑966169

gTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCAcc                                                                                                                         >  2:265482/1‑139 (MQ=255)

gTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCAcc                                                                                                                         >  1:74947/1‑139 (MQ=255)

    cAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCt                                                                                                                     >  2:638164/1‑139 (MQ=255)

    cAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCt                                                                                                                     <  1:462713/139‑1 (MQ=255)

    cAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCt                                                                                                                     <  1:541862/139‑1 (MQ=255)

        aaGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTggg                                                                                                                  >  1:338836/1‑138 (MQ=255)

          ggTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTg                                                                                                                    >  2:521073/1‑134 (MQ=255)

          ggTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTg                                                                                                                    <  1:521073/134‑1 (MQ=255)

          ggTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGaaa                                                                                                               >  1:206146/1‑139 (MQ=255)

                     aaCGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTc                                                                                                    >  1:133581/1‑139 (MQ=255)

                      aCGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCg                                                                                                   >  2:750508/1‑139 (MQ=255)

                      aCGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCg                                                                                                   >  2:548468/1‑139 (MQ=255)

                      aCGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCg                                                                                                   >  1:468061/1‑139 (MQ=255)

                           aaCGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATaa                                                                                              <  2:468061/139‑1 (MQ=255)

                               cTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGa                                                                                          >  2:44799/1‑139 (MQ=255)

                                            tACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCgg                                                                                                                       <  2:592246/97‑1 (MQ=255)

                                            tACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCgg                                                                                                                       >  1:592246/1‑97 (MQ=255)

                                            tACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGAtt                                                                             >  2:18500/1‑139 (MQ=255)

                                                tCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATg                                                                         <  1:638164/139‑1 (MQ=255)

                                                   ggCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCg                                                                                                      >  1:582323/1‑107 (MQ=255)

                                                   ggCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCg                                                                                                      <  2:582323/107‑1 (MQ=255)

                                                              aTTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGa                                                           <  1:402714/139‑1 (MQ=255)

                                                                       aCTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTgg                                                  <  1:585169/139‑1 (MQ=255)

                                                                                           gTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTc                              <  2:133581/139‑1 (MQ=255)

                                                                                                 ttAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTg                        <  1:707897/139‑1 (MQ=255)

                                                                                                          tgcCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATtg               >  2:243054/1‑139 (MQ=255)

                                                                                                          tgcCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATtg               >  1:736973/1‑139 (MQ=255)

                                                                                                          tgcCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATtg               >  2:633385/1‑139 (MQ=255)

                                                                                                                         tttACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTg  <  2:736973/137‑1 (MQ=255)

GTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTG  >  NZ_CP009273/965912‑966169

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CCTTGAAGTTATCTCTCTGTGGTTACA‑GGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTGCAACGGAAAACTT  >  NZ_CP009273/965891‑966182

CCTTGAAGTTATCTCTCTGTGGTTACAGGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGG                                                                                                                                                <  SRR3722133.325934/151‑1 (MQ=60)

          ATCTCTCTGTGGTTACA‑GGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCG                                                                                                                                     >  SRR3722133.75898/1‑151 (MQ=60)

                  GTGGTTACA‑GGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGA                                                                                                                              >  SRR3722133.343597/1‑150 (MQ=60)

                    GGTTACA‑GGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAAT                                                                                                                           >  SRR3722133.208885/1‑151 (MQ=60)

                        ACA‑GGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGAC                                                                                                                       <  SRR3722133.468991/151‑1 (MQ=60)

                        ACA‑GGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGAC                                                                                                                       <  SRR3722133.549084/151‑1 (MQ=60)

                         CA‑GGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACC                                                                                                                      <  SRR3722133.528088/151‑1 (MQ=60)

                                GGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCG                                                                                                                >  SRR3722133.135318/1‑151 (MQ=60)

                                 GTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGC                                                                                                               >  SRR3722133.474424/1‑151 (MQ=60)

                                                       GCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGctgtctcttatacacatctccgagcccacg                                                                                           >  SRR3722133.600066/1‑119 (MQ=60)

                                                              GGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGctgtctcttatacacatctccg                                                                                  >  SRR3722133.590045/1‑129 (MQ=60)

                                                                     GTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACC                                                                           <  SRR3722133.646519/151‑1 (MQ=60)

                                                                      ttttttcaagcagaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACC                                                                           <  SRR3722133.237991/78‑1 (MQ=60)

                                                                                   GATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAG                                                             <  SRR3722133.408292/151‑1 (MQ=60)

                                                                                            AACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGG                                                    <  SRR3722133.592921/151‑1 (MQ=60)

                                                                                                                     CATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGC                           >  SRR3722133.746498/1‑151 (MQ=60)

                                                                                                                      ATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCC                          <  SRR3722133.717034/151‑1 (MQ=60)

                                                                                                                                              CTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTGCAACGGAAAACTT  >  SRR3722133.701478/1‑151 (MQ=60)

CCTTGAAGTTATCTCTCTGTGGTTACA‑GGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTGCAACGGAAAACTT  >  NZ_CP009273/965891‑966182

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`