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
A5 F13 I1 R1	57	60.3	2567246	98.7%	2533871	146.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_002947_CJ‑RC	4,740,926	2 bp→CT	intergenic (+56/+696)	gltA → / ← yeiW	citrate synthase/putative oxidoreductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947_CJ‑RC	4,740,926	0	T	C	100.0%	45.6 / NA	14	intergenic (+56/+697)	gltA/yeiW	citrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (3/11); total (3/11)
*	NC_002947_CJ‑RC	4,740,927	0	G	T	100.0%	44.4 / NA	14	intergenic (+57/+696)	gltA/yeiW	citrate synthase/putative oxidoreductase
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (3/11); total (3/11)

CAGCCCGTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCCTTTTTTTATTTTTCTGGTGCCGGCCTCTTCGC‑GGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTAT  >  NC_002947_CJ‑RC/4740786‑4741025

||

cAGCCCGTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCg                                                                                               <  6:138816/147‑1 (MQ=255)

cAGCCCGTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGc                                                                                             >  6:29668/1‑149 (MQ=255)

cAGCCCGTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGc                                                                                             <  7:107925/149‑1 (MQ=255)

 aGCCCGTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGcc                                                                                            <  1:185422/149‑1 (MQ=255)

   cccGTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCgggcgc                                                                                          >  2:81586/1‑145 (MQ=255)

      gTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTc                                                                                       <  3:199222/149‑1 (MQ=255)

      gTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTc                                                                                       <  5:29668/149‑1 (MQ=255)

                  ccGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGC‑GGCCTTGccc                                                                          <  2:164602/149‑1 (MQ=255)

                       cgcgCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGC‑GGCCTTGCCCGCGaa                                                                     <  3:94206/149‑1 (MQ=255)

                        gcgcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCACTGAAAGACAGGAATTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCGTCTTCGC‑TGCCTTGCCCGCGAag                                                                    <  4:120056/149‑1 (MQ=255)

                         cgcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGC‑GGGCAAGGCCGCGAaga                                                                   <  8:94100/149‑1 (MQ=38)

                         cgcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGC‑GGCCTTGCCCGCGAaga                                                                   <  3:6568/149‑1 (MQ=255)

                          gcCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGCCTCTTCGC‑GGCCTTGCCCGCGAagag                                                                  <  5:31268/149‑1 (MQ=255)

                                                                                          aGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCC‑TTTTTTATTTGTCCTGTGCCGGGCACGTAGCGGGCATTGCCGGGGAA‑AGGGCGGGCCAGACACCCCAAAAACCCAGTTTTTTTGCGCCCCCGCCCGCCGCCCCTTAAGGGttt  >  2:171584/1‑147 (MQ=255)

||

CAGCCCGTACAAGATCGGCCGTCCGCGCCAGCTGTACACCGGCGAGCAGAAGCGCGACATCGTTGCCCTGAAAGACCGCAAGTAAGCTGCAGTAGCCGAACGCAAGAAGGCTGCCCTCGGGCAGCCTTTTTTTATTTTTCTGGTGCCGGCCTCTTCGC‑GGCCTTGCCCGCGAAGAGGCCGGCACAGACACCACAAAACCTCAGTTTTTCTCCGCCCGCTCACGCAGCCCTTTCAGGGTAT  >  NC_002947_CJ‑RC/4740786‑4741025

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A