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	1,614,031	G→A	40.6%	G115G (GGC→GGT)	eutH ←	predicted inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,614,031	0	G	A	40.6%	24.8 / 38.1	59	G115G (GGC→GGT)	eutH	predicted inner membrane protein
Reads supporting (aligned to +/- strand): ref base G (15/20); new base A (14/10); total (29/30)
Fisher's exact test for biased strand distribution p-value = 2.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAAAACACAATCGTTGGCCCCATCATCGACCCGAGAATTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTCCGGCG  >  minE/1613963‑1614094

gAAAACACAATCGTTGGCCCCATCATCGACCCGAGAATTAACCCAGAGTATAGCCACGCGGCTACGTcg                                                                 >  1:285834/1‑69 (MQ=255)

gAAAACACAATCGTTGGCCCCATCATCGACCCGAGAATTAACCCAGAGTATAGCCACGCGGCTACGTcg                                                                 >  1:1294065/1‑69 (MQ=255)

gAAAACACAATCGTTGGCCCCATCATCGACCCGAGAATTAACCCAGAGTATAGCCACGCGGCTACGTcg                                                                 >  1:459975/1‑69 (MQ=255)

            gTTGGCCCCATCATCGACCCGAGGATTAACCCAGAGTATAGCCACGCTGCTACGTCACCGCCCGCCAGc                                                     <  1:1040811/69‑1 (MQ=255)

            gTTGGCCCCATCATCGACCCGAGGATTAACCCAGAGTATAGCCACGCTGCTACGTCACCGCCCGCCAGc                                                     <  1:2877644/69‑1 (MQ=255)

            gTTGGCCCCATCATCGACCCGAGGATTAACCCAGAGTATAGCCACGCTGCTACGTCACCGCCCGCCAGc                                                     <  1:3073621/69‑1 (MQ=255)

            gTTGGCCCCATCATCGACCCGAGGATTAACCCAGAGTATAGCCACGCTGCTACGTCACCGCCCGCCAGc                                                     <  1:2558550/69‑1 (MQ=255)

            gTTGGCCCCATCATCGACCCGAGGATTAACCCAGAGTATAGCCACGCTGCTACGTCACCGCCCGCCAGc                                                     <  1:2518671/69‑1 (MQ=255)

            gTTGGCCCCATCATCGACCCGAGGATTAACCCAGAGTATAGCCACGCTGCTACGTCACCGCCCGCCAGc                                                     <  1:3247162/69‑1 (MQ=255)

            gTTGGCCCCATCATCGACCCGAGGATTAACCCAGAGTATAGCCACGCTGCTACGTCACCGCCCGCCAGc                                                     <  1:2174726/69‑1 (MQ=255)

            gTTGGCCCCATCATCGACCCGAGGATTAACCCAGAGTATAGCCACGCTGCTACGTCACCGCCCGCCAGc                                                     <  1:558411/69‑1 (MQ=255)

            gTTGGCCCCATCATCGACCCGAGGATTAACCCAGAGTATAGCCACGCTGCTACGTCACCGCCCGCCAGc                                                     <  1:571910/69‑1 (MQ=255)

            gTTGGCCCCATCATCGACCCGAGGATTAACCCAGAGTATAGCCACGCTGCTACGTCACCGCCCGCCAGc                                                     <  1:1209605/69‑1 (MQ=255)

                      tcatcGACCCGAGAATTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCg                                            >  1:2077449/1‑68 (MQ=255)

                        atcGACCCGAGAATTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGctc                                                   >  1:2307923/1‑59 (MQ=255)

                        atcGACCCGAGAATTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGa                                           >  1:2379163/1‑67 (MQ=255)

                        atcGACCCGAGAATTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGa                                           >  1:2425823/1‑67 (MQ=255)

                        atcGACCCGAGAATTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCAGCCAGCTCTTTGGCGa                                           >  1:1021468/1‑67 (MQ=255)

                                   aaTTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAgccgcc                              <  1:1958711/69‑1 (MQ=255)

                                   aaTTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAgccgcc                              <  1:309726/69‑1 (MQ=255)

                                   aaTTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAgccgcc                              <  1:2315247/69‑1 (MQ=255)

                                   aaTTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAgccgcc                              <  1:1846565/69‑1 (MQ=255)

                                   aaTTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAgccgcc                              <  1:1285021/69‑1 (MQ=255)

                                   aaTTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAgccgcc                              <  1:675968/69‑1 (MQ=255)

                                      tAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCat                           >  1:1334846/1‑69 (MQ=255)

                                      tAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCat                           >  1:2519782/1‑69 (MQ=255)

                                      tAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCat                           >  1:200344/1‑69 (MQ=255)

                                       aaCCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCat                           <  1:1916059/68‑1 (MQ=255)

                                       aaCCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCat                           <  1:2590717/68‑1 (MQ=255)

                                       aaCCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCat                           <  1:2001639/68‑1 (MQ=255)

                                          ccAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCg                       <  1:1741832/69‑1 (MQ=255)

                                          ccAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCg                       <  1:1063505/69‑1 (MQ=255)

                                                  taGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGcc                 >  1:3287873/1‑67 (MQ=255)

                                                  taGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGcc                 >  1:1929299/1‑67 (MQ=255)

                                                    gCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCcagc              <  1:2179449/68‑1 (MQ=255)

                                                    gCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCcagc              <  1:2673279/68‑1 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAgtgt         >  1:2852751/4‑68 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:3186800/4‑69 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:78595/4‑69 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:576039/4‑69 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:465927/4‑69 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:2921390/4‑69 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:2398201/4‑69 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:2644597/4‑69 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:2569926/4‑69 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:1262839/4‑69 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:127197/4‑69 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:1373226/4‑69 (MQ=255)

                                                         gctgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:2200367/4‑69 (MQ=255)

                                                         gatgCTACGTCACCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGtt        >  1:2948296/4‑69 (MQ=255)

                                                          cgGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTc       >  1:927272/1‑69 (MQ=255)

                                                          cgGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTc       >  1:2064354/1‑69 (MQ=255)

                                                          cgGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTc       >  1:2111492/1‑69 (MQ=255)

                                                          cgGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTc       >  1:233932/1‑69 (MQ=255)

                                                          cgGCTAAGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTc       >  1:436146/1‑69 (MQ=255)

                                                               aCGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTCCGGCg  <  1:20274/69‑1 (MQ=255)

                                                               aCGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTCCGGCg  <  1:1780831/69‑1 (MQ=255)

                                                               aCGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTCCGGCg  <  1:1774027/69‑1 (MQ=255)

                                                               aCGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTCCGGCg  <  1:2222364/69‑1 (MQ=255)

                                                               aCGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTCCGGCg  <  1:896359/69‑1 (MQ=255)

                                                               aCGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTCCGGCg  <  1:3001382/69‑1 (MQ=255)

                                                                cGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTCCGGCg  <  1:3097353/68‑1 (MQ=255)

GAAAACACAATCGTTGGCCCCATCATCGACCCGAGAATTAACCCAGAGTATAGCCACGCGGCTACGTCGCCGCCCGCCAGCTCTTTGGCGAGGAAGAAGCCGCCCATATCGCACGCCAGCAGTGTTCCGGCG  >  minE/1613963‑1614094

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