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 I197 R1	189	12.7	697584	97.1%	677354	86.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,849,315	A→C	Y540S (TAC→TCC)	flhA →	formate hydrogenlyase transcriptional activator FlhA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,849,315	0	A	C	100.0%	20.0 / NA	8	Y540S (TAC→TCC)	flhA	formate hydrogenlyase transcriptional activator FlhA
Reads supporting (aligned to +/- strand): ref base A (0/0); new base C (1/7); total (1/7)

GCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTT  >  NZ_CP009273/2849251‑2849399

gccgcGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCAc                                                             <  2:31963/90‑1 (MQ=255)

        tacccGCGATCTGAAAAAAATGGTCGCCGCCCGTGAGTCCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTgccgcc                                                     <  1:163197/87‑1 (MQ=255)

                  ctaaaaaaaaGGGTCGCCGCCCGTGAGTCCCGTAGCGTTCTCTTTCCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAg                                           <  1:244700/87‑1 (MQ=255)

                                               ccGTGGCGATCTCTATTCCCGCCTGAACGTATCCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGaa              <  1:228433/90‑1 (MQ=39)

                                               ccGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGaa              <  2:192866/90‑1 (MQ=255)

                                               ccGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGaa              <  2:5694/90‑1 (MQ=255)

                                                       aTCTCTTTTCCCGCCTGAACGTATCCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTa      <  1:240608/90‑1 (MQ=39)

                                                           ctATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCtt  >  1:155863/1‑90 (MQ=255)

GCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTT  >  NZ_CP009273/2849251‑2849399

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 5 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 25 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTGCC  >  NZ_CP009273/2849217‑2849409

CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCC                                                                                               <  SRR3722076.233101/100‑1 (MQ=60)

  ACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTCCCG                                                                                             <  SRR3722076.176087/100‑1 (MQ=60)

                                          TACCCGCGATCTGAAAAAAATGGTCGCCGCCCGTGAGTCCCGTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAG                                                     <  SRR3722076.165185/100‑1 (MQ=60)

                                                    CTAAAAAAAAGGGTCGCCGCCCGTGAGTCCCGTAGCGTTCTCTTTCCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAG                                           <  SRR3722076.248181/100‑1 (MQ=60)

                                                                                 CCGTGGCGATCTCTATTCCCGCCTGAACGTATCCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACC              <  SRR3722076.231570/100‑1 (MQ=60)

                                                                                   GTAGCGATCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTT            >  SRR3722076.157703/1‑100 (MQ=60)

                                                                                         ATCTCTTTTCCCGCCTGAACGTATCCCCGATTCCCCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAAT      <  SRR3722076.243999/100‑1 (MQ=60)

                                                                                          TCTCTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATT     >  SRR3722076.333079/1‑100 (MQ=60)

                                                                                             CTATTCCCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTGCC  >  SRR3722076.45765/1‑100 (MQ=60)

CAACAAAATCATTCAGACGGACGTGCGTCTAATCGCCGCGACTAACCGCGATCTGAAAAAAATGGTCGCCGACCGTGAGTTCCGTAGCGATCTCTATTACCGCCTGAACGTATTCCCGATTCACCTGCCGCCACTACGCGAGCGTCCGGAAGATATTCCGCTGCTGGCGAAAGCCTTTACCTTCAAAATTGCC  >  NZ_CP009273/2849217‑2849409

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 7 ≤` `ATCG/ATCG` `< 10 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`