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 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,717,117	G→A	37.7%	T359T (ACC→ACT)	glyA ←	serine hydroxymethyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,717,117	0	G	A	37.7%	28.6 / 30.6	53	T359T (ACC→ACT)	glyA	serine hydroxymethyltransferase
Reads supporting (aligned to +/- strand): ref base G (18/15); new base A (10/10); total (28/25)
Fisher's exact test for biased strand distribution p-value = 7.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.14e-01

TTAAAGCCGCGACGGGTAATCGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGTGATGTTAGCACGG  >  minE/1717070‑1717180

ttAAAGCCGCGACGGGTAATCGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCgg                                             <  1:2613004/68‑1 (MQ=255)

ttAAAGCCGCGACGGGTAATCGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCgg                                             <  1:2929939/68‑1 (MQ=255)

ttAAAGCCGCGACGGGTAATCGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCgg                                             <  1:1140520/68‑1 (MQ=255)

ttAAAGCCGCGACGGGTAATCGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCgg                                             <  1:3161816/68‑1 (MQ=255)

ttAAAGCCGCGACGGGTAATCGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCgg                                             <  1:281143/68‑1 (MQ=255)

ttAAAGCCGCGACGGGTAATCGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCgg                                             <  1:1692195/68‑1 (MQ=255)

ttAAAGCCGCGACGGGTAATCGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCgg                                             <  1:1688211/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTGGGATCGTTCGGTACGCTGtttt                         <  1:333503/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:959624/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         >  1:1397013/1‑68 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:2892605/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         >  1:2805111/1‑68 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:3262877/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         >  1:959988/1‑68 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         >  1:2598444/1‑68 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:2462427/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         >  1:2379304/1‑68 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:245268/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:303344/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:1253629/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:3419197/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:463377/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:3390310/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:942012/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAATACCGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:904327/68‑1 (MQ=255)

                    cGCCGGAGTACCTACACGAACACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         >  1:1367039/1‑68 (MQ=255)

                    agCCGGAGTACCTACACGAATACCGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:3302296/67‑1 (MQ=255)

                     gCCGGAGTACCTACACGAATACCGGAAGGCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:2665029/67‑1 (MQ=255)

                            tACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:2326399/60‑1 (MQ=255)

                              ccTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGt                                   >  1:642231/1‑48 (MQ=255)

                              ccTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGTg              >  1:3225685/1‑69 (MQ=255)

                              ccTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGTg              >  1:1008408/1‑69 (MQ=255)

                                    cGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGt               >  1:3414892/1‑62 (MQ=255)

                                     gAATACCGGAGGTCTCAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:278500/51‑1 (MQ=255)

                                          ccGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGtttt                         <  1:1099304/46‑1 (MQ=255)

                                          ccGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGTGATGTTAGCACgg  >  1:3193094/1‑69 (MQ=255)

                                          ccGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGTGATGTTAGCACgg  >  1:2694814/1‑69 (MQ=255)

                                          ccGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGTGATGTTAGCACgg  >  1:1856404/1‑69 (MQ=255)

                                          ccGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGTGATGTTAGCACgg  >  1:2628992/1‑69 (MQ=255)

                                          ccGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGTGATGTTAGCACgg  >  1:2598089/1‑69 (MQ=255)

                                          ccGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGTGATGTTAGCACgg  >  1:2421611/1‑69 (MQ=255)

                                          ccGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGTGATGTTAGCACgg  >  1:2171560/1‑69 (MQ=255)

                                          ccGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGTGATGATAGCACgg  >  1:2451306/1‑69 (MQ=255)

                                           cGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTCACGGTGATGTTAGCACgg  >  1:2298169/1‑68 (MQ=255)

                                           cGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTCACGGTGATGTTAGCACgg  >  1:1016895/1‑68 (MQ=255)

                                           cGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTCACGGTGATGTTAGCACgg  >  1:155033/1‑68 (MQ=255)

                                           cGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTCACGGTGATGTTAGCACgg  >  1:1965979/1‑68 (MQ=255)

                                           cGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTCACGGTGATGTTAGCACgg  >  1:536300/1‑68 (MQ=255)

                                           cGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTCACGGTGATGTTAGCACgg  >  1:2256369/1‑68 (MQ=255)

                                           cGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTCACGGTGATGTTAGCACgg  >  1:3014683/1‑68 (MQ=255)

                                           cGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTCACGGTGATGTTAGCACgg  >  1:2705520/1‑68 (MQ=255)

                                           cGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTCACGGTGATGTTAGCACgg  >  1:2862560/1‑68 (MQ=255)

                                           cGGAAGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTCACGGTGATGTTAGCACgg  >  1:2911322/1‑68 (MQ=255)

                                               ggTCACTAACGGGCTCTTCGTATCGTTCGGTACGCTGtttt                         <  1:2199617/41‑1 (MQ=255)

TTAAAGCCGCGACGGGTAATCGCCGGAGTACCTACACGAATACCGGAGGTCACAAACGGGCTCTTCGGATCGTTCGGTACGCTGTTTTTGTTGACGGTGATGTTAGCACGG  >  minE/1717070‑1717180

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A