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 I178 R1	167	28.0	1137820	95.3%	1084342	115.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	438,112	A→G	S370G (AGC→GGC)	thiI →	tRNA 4‑thiouridine(8) synthase ThiI

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	438,112	0	A	G	100.0%	104.9 / NA	29	S370G (AGC→GGC)	thiI	tRNA 4‑thiouridine(8) synthase ThiI
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (18/11); total (18/11)

TCAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGA  >  NZ_CP009273/437978‑438239

tcaACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAt                                                                                                                             <  2:241950/139‑1 (MQ=255)

  aaCCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAtt                                                                                                                            <  2:410662/138‑1 (MQ=255)

  aaCCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAtt                                                                                                                            <  1:539350/138‑1 (MQ=255)

        gCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGAt                                                                                                                      >  2:319271/1‑138 (MQ=255)

        gCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGAt                                                                                                                      >  2:441452/1‑138 (MQ=255)

        gCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGAt                                                                                                                      >  1:428504/1‑138 (MQ=255)

                             gACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATa                                                                                                <  1:25905/139‑1 (MQ=255)

                                        cACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATc                                                                                     >  1:412749/1‑139 (MQ=255)

                                                        tgtgGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCcag                                                                      >  1:356589/1‑138 (MQ=255)

                                                         gtggtgTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAt                                                                                                                             <  1:310261/82‑1 (MQ=255)

                                                         gtggtgTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCAt                                                                                                                             >  2:310261/1‑82 (MQ=255)

                                                            gtgtGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGa                                                                  <  1:75751/138‑1 (MQ=255)

                                                            gtgtGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAc                                                                 <  2:392024/139‑1 (MQ=255)

                                                            gtgtGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAc                                                                 <  2:356589/139‑1 (MQ=255)

                                                               tgATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAcc                                                                >  1:536026/1‑137 (MQ=255)

                                                               tgATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAcc                                                                >  2:232993/1‑137 (MQ=255)

                                                                 aTCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAc                                                                 <  1:324522/134‑1 (MQ=255)

                                                                 aTCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGAc                                                                 >  2:324522/1‑134 (MQ=255)

                                                                 aTCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAg                                                             >  1:41527/1‑138 (MQ=255)

                                                                    tcCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAg                                                          >  1:78631/1‑138 (MQ=255)

                                                                              cGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGtggtgg                                                >  2:469913/1‑138 (MQ=255)

                                                                                aCGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGgtggaag                                             >  1:260983/1‑139 (MQ=255)

                                                                                aCGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGgtggaag                                             >  2:7973/1‑139 (MQ=255)

                                                                                                     aaGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCg                        >  2:545885/1‑139 (MQ=255)

                                                                                                                        agaagTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCt     >  1:130807/1‑139 (MQ=255)

                                                                                                                        agaagTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCt     <  1:262340/139‑1 (MQ=255)

                                                                                                                            gTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGa         >  1:520181/1‑131 (MQ=255)

                                                                                                                            gTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGa         <  2:520181/131‑1 (MQ=255)

                                                                                                                            gTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGa  >  2:2818/1‑138 (MQ=255)

TCAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGA  >  NZ_CP009273/437978‑438239

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

TCATCAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTATCGATGAAC  >  NZ_CP009273/437975‑438259

TCATCAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATA                                                                                                                                         >  SRR3722132.436243/1‑150 (MQ=60)

  gagatctagtacggtctcgtgggctcggagatgtgtataagagacagGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAG                                                                                                                                      <  SRR3722132.316081/104‑1 (MQ=60)

    CATCCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCTGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGT                                                                                                                                     <  SRR3722132.240768/150‑1 (MQ=60)

    CAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGT                                                                                                                                     <  SRR3722132.548865/150‑1 (MQ=60)

                               AGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATC                                                                                                         <  SRR3722132.26362/151‑1 (MQ=60)

                                GATTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCC                                                                                                        >  SRR3722132.420236/1‑151 (MQ=60)

                                                TGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGC                                                                                         >  SRR3722132.363169/1‑150 (MQ=60)

                                                       ATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCG                                                                                   >  SRR3722132.545491/1‑149 (MQ=60)

                                                         ATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGC                                                                                >  SRR3722132.42285/1‑150 (MQ=60)

                                                            GTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGG                                                                             >  SRR3722132.80059/1‑150 (MQ=60)

                                                              GGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAG                                                                          <  SRR3722132.330579/151‑1 (MQ=60)

                                                              GGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAA                                                                           <  SRR3722132.77129/150‑1 (MQ=60)

                                                                        CCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGT                                                                >  SRR3722132.265944/1‑151 (MQ=60)

                                                                                                                AGCGGAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTC                        >  SRR3722132.133234/1‑151 (MQ=60)

                                                                                                                    GAAGAAGAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGAT                     >  SRR3722132.529404/1‑150 (MQ=60)

                                                                                                                          GAGAAGTTCGACTTCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTT              <  SRR3722132.267324/151‑1 (MQ=60)

                                                                                                                                       TCGGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTATCGATGAAC  <  SRR3722132.2872/150‑1 (MQ=60)

TCATCAACCTGGCCCGCCAGATTGGCACCGAAGACTTTGCTCGCACGATGCCGGAATATTGTGGTGTGATCTCCAAAAGCCCGACGGTGAAAGCAGTTAAATCGAAGATTGAAGCGGAAGAAGAGAAGTTCGACTTCAGCATTCTCGATAAAGTGGTTGAGGAAGCGAATAACGTTGATATCCGCGAAATCGCCCAGCAGACCGAGCAGGAAGTGGTGGAAGTGGAAACCGTCAATGGCTTCGGCCCGAACGACGTGATCCTCGATATCCGTTCTATCGATGAAC  >  NZ_CP009273/437975‑438259

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`