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	728,565	T→C	31.8%	S184S (AGT→AGC)	fabH →	3‑oxoacyl‑[acyl‑carrier‑protein] synthase III

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	728,565	0	T	C	31.8%	35.8 / 21.6	47	S184S (AGT→AGC)	fabH	3‑oxoacyl‑[acyl‑carrier‑protein] synthase III
Reads supporting (aligned to +/- strand): ref base T (25/7); new base C (5/10); total (30/17)
Fisher's exact test for biased strand distribution p-value = 7.67e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGAATTCAATTC  >  minE/728497‑728623

ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt                                                            <  1:1845060/69‑1 (MQ=255)

ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt                                                            >  1:1947116/1‑69 (MQ=255)

ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt                                                            <  1:854847/69‑1 (MQ=255)

ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt                                                            >  1:719249/1‑69 (MQ=255)

ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt                                                            >  1:2782660/1‑69 (MQ=255)

ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt                                                            >  1:1358730/1‑69 (MQ=255)

ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt                                                            >  1:3074882/1‑69 (MQ=255)

ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt                                                            >  1:3237160/1‑69 (MQ=255)

ggCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGt                                                            >  1:409819/1‑69 (MQ=255)

         gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa                                                    <  1:972348/68‑1 (MQ=255)

         gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa                                                    <  1:2464329/68‑1 (MQ=255)

         gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa                                                    <  1:3037171/68‑1 (MQ=255)

         gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa                                                    <  1:1395079/68‑1 (MQ=255)

         gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa                                                    <  1:636226/68‑1 (MQ=255)

         gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa                                                    <  1:681261/68‑1 (MQ=255)

         gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa                                                    <  1:69192/68‑1 (MQ=255)

         gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa                                                    <  1:831251/68‑1 (MQ=255)

         gTGCTGGCTGCCTCTGAAGAGCCGGGAATCATCTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa                                                    <  1:1083011/68‑1 (MQ=255)

           gctggctgCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTg                                                     <  1:106420/65‑1 (MQ=255)

           gctggctgCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTg                                                     <  1:1937794/65‑1 (MQ=255)

           gctggctgCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTg                                                     <  1:1933741/65‑1 (MQ=255)

                        gAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCt                                              >  1:2958788/1‑59 (MQ=255)

                        gAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCt                                              >  1:423717/1‑59 (MQ=255)

                        gAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCt                                              >  1:2668413/1‑59 (MQ=255)

                        gAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCt                                              >  1:1687263/1‑59 (MQ=255)

                             gCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACg                                >  1:2931415/1‑68 (MQ=255)

                                    atcatcTCCACCCATCTGCATGCCGACGGTAGCTATGGTGa                                                    <  1:9380/41‑1 (MQ=255)

                                    aTCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACcgc                        >  1:1601462/1‑69 (MQ=255)

                                    aTCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACcgc                        >  1:201752/1‑69 (MQ=255)

                                    aTCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACcgc                        >  1:1708350/1‑69 (MQ=255)

                                    aTCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACcgc                        >  1:1022597/1‑69 (MQ=255)

                                       atctCCACCCATCTGCATGCCGACGGTAGCTATGGTGAATTGCTGACGCTGCCTAATGCTGACCGtgtg                     >  1:61721/4‑69 (MQ=255)

                                       atctCCACCCATCTGCATGCCGACGGTAGCTATGGTGAATTGCTGACGCTGCCTAATGCTGACCGtgtg                     >  1:1278145/4‑69 (MQ=255)

                                       atctCCACCCATCTGCATGCCGACGGTAGCTATGGTGAATTGCTGACGCTGCCTAATGCTGACCGtgtg                     >  1:2914189/4‑69 (MQ=255)

                                       atctCCACCCATCTGCATGCCGACGGTAGCTATGGTGAATTGCTGACGCTGCCTAATGCTGACCGtgtg                     >  1:1847532/4‑69 (MQ=255)

                                       atctCCACCCATCTGCATGCCGACGGTAGCTATGGTGAATTGCTGACGCTGCCTAATGCTGACCGtgtg                     >  1:143009/4‑69 (MQ=255)

                                          tCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGaa                   >  1:536474/1‑68 (MQ=255)

                                          tCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGaa                   >  1:1893345/1‑68 (MQ=255)

                                          tCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGaa                   >  1:1908513/1‑68 (MQ=255)

                                                    tGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCag              >  1:1550161/1‑63 (MQ=255)

                                                    tGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCag              >  1:2212840/1‑63 (MQ=255)

                                                    tGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCag              >  1:671546/1‑63 (MQ=255)

                                                    tGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCag              >  1:271910/1‑63 (MQ=255)

                                                    tGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCag              >  1:1635547/1‑63 (MQ=255)

                                                    tGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCag              >  1:3184523/1‑63 (MQ=255)

                                                    tGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGaat         >  1:1343775/1‑68 (MQ=255)

                                                    tGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGaat         >  1:835676/1‑68 (MQ=255)

                                                    tGCATGACGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGaat         >  1:76763/1‑68 (MQ=255)

                                                          ccGACGGTAGTTATTGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGaattc       <  1:392473/64‑1 (MQ=255)

                                                          ccGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGaattcaattc  >  1:1662787/1‑69 (MQ=255)

                                                          ccGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGaattcaattc  >  1:1352956/1‑69 (MQ=255)

                                                          ccGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGaattcaattc  >  1:1310020/1‑69 (MQ=255)

                                                          ccGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGaattcaattc  >  1:232535/1‑69 (MQ=255)

                                                          ccGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGaattc       <  1:2395893/64‑1 (MQ=255)

                                                          ccGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGaattc       <  1:1365482/64‑1 (MQ=255)

                                                          ccGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGaattc       <  1:1321103/64‑1 (MQ=255)

GGCGCTGCGGTGCTGGCTGCCTCTGAAGAGCCGGGAATCATTTCCACCCATCTGCATGCCGACGGTAGTTATGGTGAATTGCTGACGCTGCCAAACGCCGACCGCGTGAATCCAGAGAATTCAATTC  >  minE/728497‑728623

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