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 I181 R1	159	32.7	1279082	96.9%	1239430	121.0

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%	117.3 / NA	31	D399G (GAT→GGT)	ycaQ	winged helix DNA‑binding protein YcaQ
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (15/16); total (15/16)

TTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTG  >  NZ_CP009273/965913‑966156

ttACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCg                                                                                                           >  1:547679/1‑139 (MQ=255)

   cAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCt                                                                                                        >  1:35340/1‑139 (MQ=255)

   cAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCt                                                                                                        <  2:184159/139‑1 (MQ=255)

       aaGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTggg                                                                                                     >  1:435289/1‑138 (MQ=255)

                  ccAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCg                                                                                         <  1:246035/139‑1 (MQ=255)

                  ccAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCg                                                                                         <  1:536223/139‑1 (MQ=255)

                     aCGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCgg                                                                                                          <  2:376955/119‑1 (MQ=255)

                     aCGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCgg                                                                                                          >  1:376955/1‑119 (MQ=255)

                     aCGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGt                                                                                        >  2:399767/1‑137 (MQ=255)

                     aCGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGt                                                                                        <  1:399767/137‑1 (MQ=255)

                     aCGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCg                                                                                      >  2:255496/1‑139 (MQ=255)

                               tGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGAt                                                                            >  2:625445/1‑139 (MQ=255)

                               tGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGA‑CCCGTCGCATAAATGAt                                                                            >  2:195127/1‑138 (MQ=255)

                                 cAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGAtt                                                                           <  1:255496/138‑1 (MQ=255)

                                 cAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGAt                                                                            <  1:59014/137‑1 (MQ=255)

                                     aaGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGAt                                                                      <  1:515405/139‑1 (MQ=255)

                                         gCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGAt                                                                      >  1:257296/1‑135 (MQ=255)

                                              gTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGa                                                                                              <  1:593326/106‑1 (MQ=255)

                                              gTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGa                                                                                              >  2:593326/1‑106 (MQ=255)

                                              gTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGA‑CCCGTCGCATAAATGATTATGATAAGATTTATg                                                            <  1:195127/139‑1 (MQ=255)

                                               tCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATg                                                            <  2:449867/139‑1 (MQ=255)

                                                   gCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCAtt                                                        <  1:625445/139‑1 (MQ=255)

                                                             aTTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGa                                              <  2:183377/139‑1 (MQ=255)

                                                                       cTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTgga                                    <  1:286618/139‑1 (MQ=255)

                                                                                ggCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATg                           >  2:596225/1‑139 (MQ=255)

                                                                                                        ctgcCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCAtt   >  2:320786/1‑139 (MQ=255)

                                                                                                         tgcCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGc                                                           <  2:532649/82‑1 (MQ=255)

                                                                                                         tgcCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGc                                                           >  1:532649/1‑82 (MQ=255)

                                                                                                         tgcCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATtg  >  2:378782/1‑139 (MQ=255)

                                                                                                           cccGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGAt                                                                      >  2:546367/1‑69 (MQ=255)

                                                                                                           cccGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGAt                                                                      <  1:546367/69‑1 (MQ=255)

TTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTG  >  NZ_CP009273/965913‑966156

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `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

TCCTTGAAGTTATCTCTCTGTGGTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTGCAACGGAAA  >  NZ_CP009273/965890‑966178

TCCTTGAAGTTATCTCTCTGTGGTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGG                                                                                                                                            >  SRR3722135.371296/1‑151 (MQ=60)

    acagGTTATCTCTCTGTGGTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGC                                                                                                                                        <  SRR3722135.253341/147‑1 (MQ=60)

            TCTCTCTGTGGTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGG                                                                                                                                >  SRR3722135.554922/1‑151 (MQ=60)

               CTCTGTGGTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTG                                                                                                                             >  SRR3722135.35811/1‑151 (MQ=60)

                   GTGGTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGA                                                                                                                          >  SRR3722135.441218/1‑150 (MQ=60)

                                 GTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGctgtctctt                                                                                                            >  SRR3722135.382225/1‑141 (MQ=60)

                                    cggagatgtgtataagagacagAAAAGGGCTACGTCAGGCGATTTCTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCAT                                                                                                         <  SRR3722135.349702/128‑1 (MQ=60)

                                    cggagatgtgtataagagacagAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCAT                                                                                                         <  SRR3722135.601082/128‑1 (MQ=60)

                                        ACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATG                                                                                                    <  SRR3722135.249531/151‑1 (MQ=60)

                                        ACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATG                                                                                                    <  SRR3722135.543316/151‑1 (MQ=60)

                                         CCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGA                                                                                                   <  SRR3722135.405303/151‑1 (MQ=60)

                                                     CTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATA                                                                                           >  SRR3722135.260963/1‑147 (MQ=60)

                                                       GCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATT                                                                                      <  SRR3722135.259134/150‑1 (MQ=60)

                                                       GCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGAT                                                                                       <  SRR3722135.59800/149‑1 (MQ=60)

                                                           gaagacggcatacgagatctagtacggtctcgtgggctcggagatgtgtataagagacagTTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGC                                                                                 <  SRR3722135.553598/91‑1 (MQ=60)

                                                           AAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGC                                                                                 <  SRR3722135.522264/151‑1 (MQ=60)

                                                                    CGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGA‑CCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACC                                                                       <  SRR3722135.197885/151‑1 (MQ=60)

                                                                         GGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGAT                                                                   <  SRR3722135.633606/151‑1 (MQ=60)

                                                                                             ACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGA                                               <  SRR3722135.290732/151‑1 (MQ=60)

                                                                                                                     CATTAGGATGCTGCCCGCAAGGCCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCctgtctcttatacacatctccgagcccacgagaccgtactagatctc                       >  SRR3722135.539698/1‑104 (MQ=60)

                                                                                                                                           CCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTGCAACGGAAA  >  SRR3722135.216709/1‑150 (MQ=60)

                                                                                                                                           CCTCTTTACTGGTTGCCGCACCGGCTGGGAAATAGACCCCGTCACATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTGCAACGGAAA  >  SRR3722135.564442/1‑150 (MQ=60)

TCCTTGAAGTTATCTCTCTGTGGTTACAGGAAGGTATTAAACCAACGACAACGCTGCAAAAAGGGCTACGTCAGGCGATTACTGATTTCGCTAACTGGCAGCAGGCAACGCGGGTGACATTAGGATGCTGCCCGCAAGGCCTCTTTACTGATTGCCGCACCGGCTGGGAAATAGACCCCGTCGCATAAATGATTATGATAAGATTTATGCATTCATAACCCGATCCATCTGGAGGAACTATGGATCATCGTCTGCTTGAAATCATTGCCTGCCCGGTTTGCAACGGAAA  >  NZ_CP009273/965890‑966178

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`