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	1,951,476	T→G	54.1%	Q37P (CAG→CCG)	visC ←	predicted oxidoreductase, FAD/NAD(P)‑binding domain

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,951,476	0	T	G	54.1%	16.2 / 60.9	61	Q37P (CAG→CCG)	visC	predicted oxidoreductase, FAD/NAD(P)‑binding domain
Reads supporting (aligned to +/- strand): ref base T (8/20); new base G (22/11); total (30/31)
Fisher's exact test for biased strand distribution p-value = 4.58e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.41e-01

GGCATTGATAGCCGAAACGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGCCACAGGCAACCGCC  >  minE/1951421‑1951538

ggcATTGATAGCCGAAACGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTGTACGCGCTGCTc                                                   <  1:411206/69‑1 (MQ=255)

      gATAGCCGAAACGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTg                                                               <  1:993307/51‑1 (MQ=255)

      gATAGCCGAAACGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTg                                                               >  1:2412717/1‑51 (MQ=255)

      gATAGCCGAAACGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTg                                                               >  1:1863645/1‑51 (MQ=255)

      gATAGCCGAAACGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTg                                                               <  1:2704715/51‑1 (MQ=255)

      gATAGCCGAAACGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTg                                                               <  1:1634202/51‑1 (MQ=255)

      gATAGCCGAAACGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTg                                                               >  1:35804/1‑51 (MQ=255)

      gATAGCCGAAACGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTg                                                               >  1:132605/1‑51 (MQ=255)

      gATAGCCGAAACGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTg                                                               <  1:811739/51‑1 (MQ=255)

      gATAGCCGAAACGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTg                                                               <  1:892463/51‑1 (MQ=255)

              aaaCGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTGTACGCGCTGCTCCAGTACGGCAAcgc                                     <  1:520443/69‑1 (MQ=255)

              aaaCGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTGTACGCGCTGCTCCAGTACGGCAAcgc                                     <  1:2999246/69‑1 (MQ=255)

              aaaCGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTGTACGCGCTGCTCCAGTACGGCAAcgc                                     <  1:2550402/69‑1 (MQ=255)

              aaaCGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTGTACGCGCTGCTCCAGTACGGCAAcgc                                     <  1:2404709/69‑1 (MQ=255)

                      aGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCg                             <  1:2365817/69‑1 (MQ=255)

                                gtgCATCCGCCGCCAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTa                   <  1:1225700/69‑1 (MQ=255)

                                gtgCATCCGCCGCCAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTa                   <  1:2308080/69‑1 (MQ=255)

                                gtgCATCCGCCGCCAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTa                   <  1:3341875/69‑1 (MQ=255)

                                gtgCATCCGCCGCCAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTa                   <  1:639767/69‑1 (MQ=255)

                                gtgCATCCGCCGCCAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTa                   <  1:1223040/69‑1 (MQ=255)

                                gtgCATCCGCCGCCAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTa                   <  1:1303641/69‑1 (MQ=255)

                                gtgCATCCGCCGCCAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTa                   <  1:132694/69‑1 (MQ=255)

                                gtgCATCCGCCGCCAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTa                   <  1:202378/69‑1 (MQ=255)

                                gtgCATCCGCCGCCAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTa                   <  1:1461741/69‑1 (MQ=255)

                                 tgCATTCGCCGCCAGAGGTTCCTGTACGCGCTGCTCCAGTAc                                             >  1:1910639/1‑42 (MQ=255)

                                 tgCATCCGCCGCCAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTa                   <  1:3082234/68‑1 (MQ=255)

                                   cATTCGCCGCCAGAGGTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGc                <  1:1238452/69‑1 (MQ=255)

                                   cATTCGCCGCCAGAGGTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGc                <  1:544402/69‑1 (MQ=255)

                                   cATCCGCCGCCAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTa                   <  1:213260/66‑1 (MQ=255)

                                     ttCGCCGCCAGAGGTTCCTCTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGc                >  1:407734/1‑67 (MQ=255)

                                       cgccgcCAGAGGTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGCcaca            >  1:2119486/1‑69 (MQ=255)

                                       cgccgcCAGAGGTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGCcaca            >  1:1887771/1‑69 (MQ=255)

                                            ccAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGCCGCAGGCa        >  1:2050309/1‑68 (MQ=255)

                                            ccAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCcgca            >  1:3346321/1‑64 (MQ=255)

                                            ccAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCaa       >  1:59604/1‑69 (MQ=255)

                                            ccAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCaa       >  1:2300611/1‑69 (MQ=255)

                                            ccAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCaa       >  1:767417/1‑69 (MQ=255)

                                            ccAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCaa       >  1:3180624/1‑69 (MQ=255)

                                            ccAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCaa       >  1:2615828/1‑69 (MQ=255)

                                            ccAGAGGTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCa        >  1:98736/1‑68 (MQ=255)

                                               gagGTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGCCACAGGCAACCg    <  1:656618/69‑1 (MQ=255)

                                                 ggTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGCCACAGGCAACCGcc  <  1:1920909/69‑1 (MQ=255)

                                                 ggTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGCCACAGGCAACCGcc  <  1:1242524/69‑1 (MQ=255)

                                                 ggTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGCCACAGGCAACCGcc  <  1:961510/69‑1 (MQ=255)

                                                 ggTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGCCACAGGCAACCGcc  <  1:1786084/69‑1 (MQ=255)

                                                 ggTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGCCACAGGCAACCGcc  <  1:401210/69‑1 (MQ=255)

                                                 ggTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGCCACAGGCAACCGcc  <  1:521648/69‑1 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:2192926/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:964690/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:2252680/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:1435301/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:551033/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:421245/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:2604217/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:1439847/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:1451635/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:3132382/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:294959/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:2656311/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:2655350/1‑69 (MQ=255)

                                                 ggTTCCGGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTACCCTGTAAGCCGCAGGCAACCGcc  >  1:2611291/1‑69 (MQ=255)

GGCATTGATAGCCGAAACGCGCAGTTGTGGTGGTGCATTCGCCGCCAGAGGTTCCTGTACGCGCTGCTCCAGTACGGCAACGCGTAAGCCGCTCCCCTGTAAGCCACAGGCAACCGCC  >  minE/1951421‑1951538

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