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 I184 R1	278	29.6	1166432	97.3%	1134938	124.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	753,287	G→A	S48N (AGC→AAC)	sdhB →	succinate dehydrogenase iron‑sulfur subunit SdhB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	753,287	0	G	A	100.0%	76.0 / NA	23	S48N (AGC→AAC)	sdhB	succinate dehydrogenase iron‑sulfur subunit SdhB
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (12/11); total (12/11)

ATGTTGATGATGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAGCCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCCCGATTTCGGCACTCAACCAGCCGGGCAAGAAGATTGTGATTCGCC  >  NZ_CP009273/753182‑753421

aTGTTGATGATGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGgtgt                                                                                                       >  2:564001/1‑139 (MQ=255)

                gcgTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGt                                                                                       >  2:447073/1‑139 (MQ=255)

                 cgTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTc                                                                                      >  2:193252/1‑139 (MQ=255)

                             tACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCg                                                                                            >  2:58636/1‑121 (MQ=255)

                             tACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCg                                                                                            <  1:58636/121‑1 (MQ=255)

                                 cccTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGc                                                                        >  1:106713/1‑137 (MQ=255)

                                  ccTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGc                                                                        >  2:62787/1‑136 (MQ=255)

                                    tGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGaa                                                                   >  1:555529/1‑139 (MQ=255)

                                    tGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGaa                                                                   >  2:162102/1‑139 (MQ=255)

                                    tGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGaa                                                                   >  2:492393/1‑139 (MQ=255)

                                    tGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGa                                                                    <  1:536590/138‑1 (MQ=255)

                                    tGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGa                                                                    >  2:536590/1‑138 (MQ=255)

                                        aGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGt                                                               <  1:398795/139‑1 (MQ=255)

                                           ggATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTg                                                            <  2:502098/139‑1 (MQ=255)

                                             aTGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGc                                                          <  1:564001/139‑1 (MQ=255)

                                             aTGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGc                                                          <  1:447073/139‑1 (MQ=255)

                                             aTGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGc                                                          <  1:420250/139‑1 (MQ=255)

                                                       cgACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTAcc                                                <  1:492393/139‑1 (MQ=255)

                                                                    ctgGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGa                                                                    >  1:429812/1‑106 (MQ=255)

                                                                    ctgGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGa                                                                    <  2:429812/106‑1 (MQ=255)

                                                                                    aGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCCCGATTTCGGCACTCAACCAGCCGGGCaa                   <  1:193252/139‑1 (MQ=255)

                                                                                      cTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCCCGATTTCGGCACTCAACCAGCCGGGCaag                  >  1:383211/1‑138 (MQ=255)

                                                                                                      ccAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCCCGATTTCGGCACTCAACCAGCCGGGCAAGAAGATTGTGATTCGcc  <  2:177905/138‑1 (MQ=255)

ATGTTGATGATGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAGCCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCCCGATTTCGGCACTCAACCAGCCGGGCAAGAAGATTGTGATTCGCC  >  NZ_CP009273/753182‑753421

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `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

TGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAGCCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCCCGATTTCGGCACTCAACCAGCCGGGCAAGAAGATTGTGATTCGCCCGCTGCCAGG  >  NZ_CP009273/753192‑753431

agagacagGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAAC                                                                                           <  SRR3722139.59301/143‑1 (MQ=60)

            GCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCA                                                                                 >  SRR3722139.108022/1‑149 (MQ=60)

               GGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAAT                                                                            >  SRR3722139.561903/1‑151 (MQ=60)

                        CCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCC                                                                   <  SRR3722139.542752/151‑1 (MQ=60)

                             AAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTAT                                                              <  SRR3722139.403521/151‑1 (MQ=60)

                                  GATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCC                                                         <  SRR3722139.425217/151‑1 (MQ=60)

                                  GATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCC                                                         <  SRR3722139.452315/151‑1 (MQ=60)

                                  GATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCC                                                         <  SRR3722139.570473/151‑1 (MQ=60)

                                            GCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCCCGATTTCGGC                                               <  SRR3722139.498095/151‑1 (MQ=60)

                                               ACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCctgtctcttatacacatctccg                                             >  SRR3722139.434853/1‑128 (MQ=60)

                                                                 CGCTTATCCAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCCCGATTTCGGCACTCAACCAGCCGGGCAAGA                           >  SRR3722139.387780/1‑150 (MQ=60)

                                                                         CAGCTAAAAGAGAAAGATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCCCGATTTCGGCACTCAACCAGCCGGGCAAGAAGATTGTGA                  <  SRR3722139.195636/151‑1 (MQ=60)

                                                                                         ATCCCAACCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCCCGATTTCGGCACTCAACCAGCCGGGCAAGAAGATTGTGATTCGCCCGCTGCCAGG  >  SRR3722139.333625/1‑151 (MQ=60)

TGCTCCGCGTATGCAGGATTACACCCTGGAAGCGGATGAAGGTCGCGACATGATGCTGCTGGATGCGCTTATCCAGCTAAAAGAGAAAGATCCCAGCCTGTCGTTCCGCCGCTCCTGCCGTGAAGGTGTGTGCGGTTCCGACGGTCTGAACATGAACGGCAAGAATGGTCTGGCCTGTATTACCCCGATTTCGGCACTCAACCAGCCGGGCAAGAAGATTGTGATTCGCCCGCTGCCAGG  >  NZ_CP009273/753192‑753431

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`