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
A1 F2 I210 R1	226	19.6	1130256	95.4%	1078264	84.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	1,223,232	(A)_8→7	coding (63/294 nt)	BW25113_RS06140 →	YcgL domain‑containing protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	1,223,225	0	A	.	100.0%	41.6 / NA	11	coding (56/294 nt)	BW25113_RS06140	YcgL domain‑containing protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base . (8/3); total (8/3)

TGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGAT  >  NZ_CP009273/1223138‑1223310

tGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGaaa                                                                                     <  1:318612/90‑1 (MQ=255)

                 ttAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTcgc                                                                   >  2:275856/1‑90 (MQ=255)

                                aTGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAc                                                    >  1:416757/1‑90 (MQ=255)

                                  gTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACtg                                                  >  1:563670/1‑90 (MQ=255)

                                       gtgtgATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGaa                                             >  1:167391/1‑90 (MQ=255)

                                                  cGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGATGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTc                                  <  2:378089/90‑1 (MQ=255)

                                                      gcagcaAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCgt                                                                 <  1:243913/55‑1 (MQ=255)

                                                      gcagcaAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCgt                                                                 >  2:243913/1‑55 (MQ=255)

                                                      gcagcaAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGcc                              <  2:512166/90‑1 (MQ=255)

                                                                           aTTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGcc         >  2:154178/1‑90 (MQ=255)

                                                                                tatGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTgg    >  1:35942/1‑90 (MQ=255)

                                                                                  tGTCG‑AAAAAAAGACGATTTTTCGCGTGTCCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGAt  >  2:519324/1‑90 (MQ=255)

TGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGAT  >  NZ_CP009273/1223138‑1223310

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

TGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGG  >  NZ_CP009273/1223138‑1223312

TGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGAT                                                                            <  SRR3722092.324243/100‑1 (MQ=60)

                   agcgtcagatgtgtataagagacaGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGG                                                         <  SRR3722092.247864/76‑1 (MQ=60)

                      GAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAAC                                                      >  SRR3722092.424811/1‑100 (MQ=60)

                        GTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTG                                                    >  SRR3722092.574974/1‑100 (MQ=60)

                             AGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAA                                               >  SRR3722092.170191/1‑100 (MQ=60)

                                                                      GACCTATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGG      >  SRR3722092.36560/1‑100 (MQ=60)

                                                                          TATTTATATGTCG‑AAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGG  >  SRR3722092.79439/1‑100 (MQ=60)

TGCCAAAACCTGGCATCTTAAAGAGTAAAAGTATGTTTTGTGTGATTTATCGAAGCAGCAAGCGTGACCAGACCTATTTATATGTCGAAAAAAAAGACGATTTTTCGCGTGTTCCTGAGGAACTGATGAAAGGTTTTGGTCAGCCTCAGTTAGCGATGATTCTGCCGCTGGATGG  >  NZ_CP009273/1223138‑1223312

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`