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	796,792	A→G	D193G (GAT→GGT)	ybhH →	4‑oxalomesaconate tautomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	796,792	0	A	G	100.0%	87.5 / NA	24	D193G (GAT→GGT)	ybhH	4‑oxalomesaconate tautomerase
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (12/12); total (12/12)

AATTGACGGCGTACCGGGTACTGCCGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGATATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTGAATCTATCCGTCTACAAGCGGGTA  >  NZ_CP009273/796658‑796920

aaTTGACGGCGTACCGGGTACTGCCGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATg                                                                                                                              >  2:538341/1‑139 (MQ=255)

                     tGCCGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCattatt                                                                                                         >  1:351327/1‑139 (MQ=255)

                       ccGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTc                                                                                                        <  1:608523/138‑1 (MQ=255)

                        cGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCg                                                                                                      >  1:60343/1‑139 (MQ=255)

                                            tCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGaaaaa                                                                                   <  2:60343/138‑1 (MQ=255)

                                            tCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGaaaaa                                                                                   >  1:521411/1‑138 (MQ=255)

                                                 aaTGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAgg                                                                               <  1:492133/137‑1 (MQ=255)

                                                    gCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTAt                                                                           >  1:529387/1‑138 (MQ=255)

                                                      cGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGaa                                                                        <  1:538341/139‑1 (MQ=255)

                                                      cGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGaa                                                                        >  2:469248/1‑139 (MQ=255)

                                                      cGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGaa                                                                        >  2:236812/1‑139 (MQ=255)

                                                             aCCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACcgg                                                                 <  2:521411/139‑1 (MQ=255)

                                                                  aaCCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTg                                                                                          >  2:145668/1‑109 (MQ=255)

                                                                  aaCCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTg                                                                                          <  1:145668/109‑1 (MQ=255)

                                                                               ttCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGAc                                                <  2:547663/138‑1 (MQ=255)

                                                                                             tCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGcc                                 <  2:489651/139‑1 (MQ=255)

                                                                                                 attgattATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCa                             >  1:571930/1‑139 (MQ=255)

                                                                                                     attattTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTg                          >  2:249029/1‑138 (MQ=255)

                                                                                                     attattTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTg                          >  1:557832/1‑138 (MQ=255)

                                                                                                            tGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTGAATCTAt                   <  2:463353/138‑1 (MQ=255)

                                                                                                            tGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTGAATCTAt                   <  1:193455/138‑1 (MQ=255)

                                                                                                             gACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTGAATCTATc                  <  1:236812/138‑1 (MQ=255)

                                                                                                                    tCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTGAATCTATCCGTCTAc           >  2:577309/1‑138 (MQ=255)

                                                                                                                            aCCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTGAATCTATCCGTCTACAAGCGGGTa  <  2:254112/139‑1 (MQ=255)

AATTGACGGCGTACCGGGTACTGCCGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGATATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTGAATCTATCCGTCTACAAGCGGGTA  >  NZ_CP009273/796658‑796920

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

GAGGGTAGCGCCAGAATTGACGGCGTACCGGGTACTGCCGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGATATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTGAATCTATCCGTCTACAAGC  >  NZ_CP009273/796644‑796915

GAGGGTAGCGCCAGAATTGACGGCGTACCGGGTACTGCCGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTA                                                                                                                           <  SRR3722135.419231/151‑1 (MQ=60)

                        GTACCGGGTACTGCCGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTC                                                                                                   >  SRR3722135.356289/1‑151 (MQ=60)

                           CCGGGTACTGCCGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGG                                                                                                >  SRR3722135.61144/1‑151 (MQ=60)

                                    GCCGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCctgtctcttatacacatctccgagcccacg                                                                                         >  SRR3722135.419519/1‑119 (MQ=60)

                                    GCCGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATAT                                                                                        <  SRR3722135.616474/150‑1 (MQ=60)

                                               TGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAAC                                                                             >  SRR3722135.528320/1‑150 (MQ=60)

                                                 gagatgtgtataagagacagGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGG                                                                          <  SRR3722135.147708/131‑1 (MQ=60)

                                                       CTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATG                                                                     >  SRR3722135.536394/1‑150 (MQ=60)

                                                              GAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTAC                                                               <  SRR3722135.498727/149‑1 (MQ=60)

                                                                   CCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGA                                                        <  SRR3722135.545465/151‑1 (MQ=60)

                                                                          AACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGctgtctcttatacacatctccgagcccacgagaccgtactagatctcgtatgccgtcttctgcttgaa                                                  >  SRR3722135.83038/1‑82 (MQ=60)

                                                                                             agatctagtacggtctcgtgggctcggagatgtgtataagagacagCCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAG                              <  SRR3722135.325467/105‑1 (MQ=60)

                                                                                                    CTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCAT                       >  SRR3722135.579451/1‑151 (MQ=60)

                                                                                                        TAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTGA                    >  SRR3722135.565203/1‑150 (MQ=60)

                                                                                                                         TTGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTGAATCTATCCGTCTACAAG   <  SRR3722135.196196/150‑1 (MQ=60)

                                                                                                                          TGACGATGTCCCGGTGACCTGTATCGGTATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTGAATCTATCCGTCTACAAGC  <  SRR3722135.240166/150‑1 (MQ=60)

GAGGGTAGCGCCAGAATTGACGGCGTACCGGGTACTGCCGCACCGGTTGCGCTCACTTTCCTGAATGCCGCTGGAACCAAAACCGGAAAAGTTTTCCCGACTGATAATCAGATTGATTATTTTGACGATGTCCCGGTGACCTGTATCGATATGGCGATGCCAGTCGTCATTATTCCGGCTGAATATCTGGGAAAAACAGGTTATGAATTACCGGCGGAACTGGATGCCGACAAAGCATTATTAGCCCGCATTGAATCTATCCGTCTACAAGC  >  NZ_CP009273/796644‑796915

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`