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 I82 R1	8	11.7	688212	96.3%	662748	85.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,754,231	G→T	R127S (CGC→AGC)	selA ←	L‑seryl‑tRNA(Sec) selenium transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,754,231	0	G	T	100.0%	50.6 / NA	15	R127S (CGC→AGC)	selA	L‑seryl‑tRNA(Sec) selenium transferase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (9/6); total (9/6)

CATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCGTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGG  >  NZ_CP009273/3754150‑3754290

cATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt                                                     <  1:172142/90‑1 (MQ=255)

cATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGcgt                                                     <  2:165207/90‑1 (MQ=255)

     ttATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTcc                                                <  1:155286/90‑1 (MQ=255)

              aTACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATAc                                       >  1:58855/1‑90 (MQ=255)

              aTACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATAc                                       >  2:149531/1‑90 (MQ=255)

              aTACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATAc                                       >  2:1710/1‑90 (MQ=255)

                    gCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAgg                                 >  1:171181/1‑90 (MQ=255)

                      aTCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGt                               >  2:319511/1‑90 (MQ=255)

                      aTCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGt                               >  2:337281/1‑90 (MQ=255)

                        cTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCa                             >  1:1266/1‑90 (MQ=255)

                        cTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCa                             >  2:327722/1‑90 (MQ=255)

                               ccccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGa                      <  1:149531/90‑1 (MQ=255)

                               ccccGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGa                      <  1:337281/90‑1 (MQ=255)

                                          ggCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCt           >  2:320578/1‑90 (MQ=255)

                                                   gcTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACgg  <  2:130993/90‑1 (MQ=255)

CATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCGTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCCTGCGCAACGG  >  NZ_CP009273/3754150‑3754290

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 23 ≤` `ATCG/ATCG` `< 30 ≤` `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

CATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCGTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCC  >  NZ_CP009273/3754150‑3754280

CATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATC                                 <  SRR3722221.174728/100‑1 (MQ=60)

    GTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATAC                             >  SRR3722221.59690/1‑100 (MQ=60)

     TTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACT                            <  SRR3722221.157469/100‑1 (MQ=60)

          GACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGG                       >  SRR3722221.173746/1‑100 (MQ=60)

              ATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCA                   >  SRR3722221.1278/1‑100 (MQ=60)

                               CCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCC  <  SRR3722221.151543/100‑1 (MQ=60)

                               CCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCTTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCC  <  SRR3722221.343338/100‑1 (MQ=60)

CATTGTTATTGACGATACAGGCATCTTCCGCCCCCGTAATACGGCACAGCAGCTGCGCCAGCGCCCGATCGCGATGTCCGCGTCCGGCGTCGTCCAGATCATACTCGAGGGTCACTGGCGAACGCATAGCC  >  NZ_CP009273/3754150‑3754280

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 26 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`