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 I214 R1	12	15.1	924212	96.1%	888167	85.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	690,117	C→T	V99I (GTC→ATC)	miaB ←	tRNA (N6‑isopentenyl adenosine(37)‑C2)‑methylthiotransferase MiaB

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	690,117	0	C	T	92.9%	42.1 / ‑3.3	14	V99I (GTC→ATC)	miaB	tRNA (N6‑isopentenyl adenosine(37)‑C2)‑methylthiotransferase MiaB
Reads supporting (aligned to +/- strand): ref base C (0/1); new base T (11/2); total (11/3)
Fisher's exact test for biased strand distribution p-value = 2.14e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01

GGGCTGCGGTCGCCACGCACGGAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGACATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATC  >  NZ_CP009273/690041‑690184

gggCTGCGGTCGCCACGCACGGAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGgcgcgc                                                        >  2:51553/1‑90 (MQ=255)

  gCTGCGGTCGCCACGCACGGAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTg                                                      >  2:308191/1‑90 (MQ=255)

               cgcacgGAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCg                                         >  2:328531/1‑90 (MQ=255)

                               tctcCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCa                         >  1:412010/1‑90 (MQ=255)

                                         aCGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCAcc               >  1:131802/1‑90 (MQ=255)

                                         aCGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCAcc               >  2:30165/1‑90 (MQ=255)

                                                      tGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATc  >  1:141836/1‑90 (MQ=255)

                                                      tGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATc  >  1:145943/1‑90 (MQ=255)

                                                      tGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATc  >  1:432685/1‑90 (MQ=255)

                                                      tGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATc  >  2:119741/1‑90 (MQ=255)

                                                      tGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATc  <  2:141836/90‑1 (MQ=255)

                                                      tGCGGCCCAAAAATAATATCGACATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATc  <  1:412171/90‑1 (MQ=255)

                                                                    aataTCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAg                    <  1:33851/58‑1 (MQ=255)

                                                                    aataTCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAg                    >  2:33851/1‑58 (MQ=255)

GGGCTGCGGTCGCCACGCACGGAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGACATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATC  >  NZ_CP009273/690041‑690184

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 29 ≤` `ATCG/ATCG` `< 33 ≤` `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

GAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGACATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATCAGGTCTGGATTCTTCTC  >  NZ_CP009273/690062‑690201

GAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCA                                          >  SRR3722097.417788/1‑100 (MQ=60)

          TCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACC                                >  SRR3722097.133361/1‑100 (MQ=60)

               cggagatgtgtataagagacaGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGC                           <  SRR3722097.34242/79‑1 (MQ=60)

                       GTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATC                   >  SRR3722097.143494/1‑100 (MQ=60)

                       GTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATC                   >  SRR3722097.147644/1‑100 (MQ=60)

                       GTGCAGCGTTTGCGGCCCAAAAATAATATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATC                   >  SRR3722097.438753/1‑100 (MQ=60)

                                 TGCGGCCCAAAAATAATATCGACATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATCAGGTCTGGAT         <  SRR3722097.417954/100‑1 (MQ=60)

                                        taagagacagATCGATATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATCAGGTCTGGATTCTTCTC  <  SRR3722097.404609/90‑1 (MQ=60)

GAGTTGATCATCTCCGGCAGACGGTGCAGCGTTTGCGGCCCAAAAATAATATCGACATAGTGGGCGCGCTGGCGAATGTGCTCGCCTTCTTGCGATGCCACGCAGCCACCGACGCCGATAATCAGGTCTGGATTCTTCTC  >  NZ_CP009273/690062‑690201

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`