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
A2 F28 I1 R2	146	74.7	3299319	84.8%	2797822	66.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	minE	1,509,579	G→A	A42T (GCA→ACA)	ackA →	acetate kinase A and propionate kinase 2

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,509,579	0	G	A	98.2%	179.5 / NA	54	A42T (GCA→ACA)	ackA	acetate kinase A and propionate kinase 2
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (9/44); minor base T (0/1); total (9/45)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAGCACGTATCAAATGGAAAATGGACGGCAATAAACAGG > minE/1509533‑1509615

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:2987100/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:2229569/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:2448167/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:2729493/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:2803530/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:2839124/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:2870527/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:2874151/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:2936150/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:2541955/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:3006223/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:3187841/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:3241848/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:3256744/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:335435/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:590581/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:715654/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:951071/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:1847003/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:1188479/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:1323366/71‑1 (MQ=255)

tGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACg              <  1:1892103/71‑1 (MQ=255)

 gAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACgg             >  1:1561762/1‑71 (MQ=255)

 gAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACgg             >  1:706235/1‑71 (MQ=255)

 gAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACgg             >  1:1845325/1‑71 (MQ=255)

 gAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACgg             >  1:2406087/1‑71 (MQ=255)

 gAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACgg             >  1:3193785/1‑71 (MQ=255)

 gAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACgg             >  1:1973468/1‑71 (MQ=255)

 gAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACgg             >  1:1957054/1‑71 (MQ=255)

   agagTACCTTTCTGGTTTAGTCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:1057904/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:125231/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:1227951/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:554991/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:600883/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:6464/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:166492/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:3141853/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:3111968/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:3100891/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:2181450/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:1836175/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:185245/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:2860048/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:1016084/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:1988078/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:2440701/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:2312891/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:2282289/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:2088408/71‑1 (MQ=255)

   agagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:2198454/71‑1 (MQ=255)

    gagTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCa           <  1:375709/70‑1 (MQ=255)

              cTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCAATAAACAgg  >  1:2474456/1‑69 (MQ=255)

              cTGGTTTAGCCGAATGTTTCCACCTGCCCGAAACACGTATCAAATGGAAAATGGACGGCAATAAACAgg  >  1:558732/1‑69 (MQ=255)

                                  cACCTGCCCGAATCACGTATCAAATGGAAAATGGACg              <  1:10959/37‑1 (MQ=255)

TGAAGAGTACCTTTCTGGTTTAGCCGAATGTTTCCACCTGCCCGAAGCACGTATCAAATGGAAAATGGACGGCAATAAACAGG > minE/1509533‑1509615

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A