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	349,604	T→C	49.3%	F36F (TTT→TTC)	hyi →	hydroxypyruvate isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	349,604	0	T	C	49.3%	‑6.3 / 59.1	65	F36F (TTT→TTC)	hyi	hydroxypyruvate isomerase
Reads supporting (aligned to +/- strand): ref base T (6/27); new base C (14/18); total (20/45)
Fisher's exact test for biased strand distribution p-value = 3.32e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATATGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACA  >  minE/349538‑349663

atatGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTc                                                            <  1:1209106/68‑1 (MQ=255)

 tatGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCt                                                          <  1:96306/69‑1 (MQ=255)

 tatGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCt                                                          <  1:2081559/69‑1 (MQ=255)

 tatGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCt                                                          >  1:2892769/1‑69 (MQ=255)

 tatGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCt                                                          <  1:2983342/69‑1 (MQ=255)

  atGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCt                                                          <  1:641068/68‑1 (MQ=255)

  atGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCt                                                          <  1:3353619/68‑1 (MQ=255)

  atGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCt                                                          <  1:3306084/68‑1 (MQ=255)

  atGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCt                                                          <  1:722249/68‑1 (MQ=255)

  atGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCt                                                          <  1:1018935/68‑1 (MQ=255)

  atGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCt                                                          <  1:2400333/68‑1 (MQ=255)

        ttCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCt                                                          >  1:2207664/1‑62 (MQ=255)

        ttCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACt                                                   <  1:596685/69‑1 (MQ=255)

        ttCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACt                                                   <  1:2085667/69‑1 (MQ=255)

           tcGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTAc                                                 <  1:3166713/68‑1 (MQ=255)

           tcGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTAc                                                 <  1:731868/68‑1 (MQ=255)

           tcGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTAc                                                 <  1:2649406/68‑1 (MQ=255)

            cGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTAc                                                 <  1:2452086/67‑1 (MQ=255)

                              tGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACa                             <  1:3130548/69‑1 (MQ=255)

                              tGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACa                             <  1:25949/69‑1 (MQ=255)

                              tGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACa                             <  1:2254100/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACa                             <  1:2997660/58‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCg                   >  1:2462814/1‑68 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCg                   >  1:1731509/1‑68 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCg                   >  1:742558/1‑68 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCg                   >  1:1805297/1‑68 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:808862/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:885094/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:3217797/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:1139187/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:382569/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:894992/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:366977/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:358959/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:1257782/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:3235472/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:1040348/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:2253406/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:2882992/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:2297541/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:2838230/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:2466888/69‑1 (MQ=255)

                                         gTTTTCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:2476642/69‑1 (MQ=255)

                                          ttttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGa                  <  1:1552252/68‑1 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAg                 >  1:2199334/1‑68 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAg                 >  1:1461418/1‑68 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAg                 >  1:48266/1‑68 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAGt                >  1:3007532/1‑69 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAGt                >  1:2225028/1‑69 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAGt                >  1:762532/1‑69 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAGt                >  1:664266/1‑69 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAGt                >  1:115401/1‑69 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAGt                >  1:55438/1‑69 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAGt                >  1:456353/1‑69 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAGt                >  1:263644/1‑69 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAGt                >  1:3299851/1‑69 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCTGGCGAGt                >  1:1346128/1‑69 (MQ=255)

                                           tttCGCGGCGTTGAATTTATGTTCCCTTATGACTACGACATTGAAGAATTAAAACAGGTGCCGGCGAg                 >  1:1913994/1‑68 (MQ=255)

                                            ttCGCGGCGTTGAATTTATGTTTCCTTATGACTAc                                                 <  1:1258785/35‑1 (MQ=255)

                                                     ttGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACa                             <  1:815621/46‑1 (MQ=255)

                                                          tttATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACa  <  1:118018/68‑1 (MQ=255)

                                                          tttATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACa  <  1:534630/68‑1 (MQ=255)

                                                          tttATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACa  <  1:1089830/68‑1 (MQ=255)

                                                          tttATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACa  <  1:2267546/68‑1 (MQ=255)

                                                          tttATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACa  <  1:1444041/68‑1 (MQ=255)

ATATGATTTTCTCGCCCGTTTTGAGAAAGCTGCGCAGTGTGGTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACA  >  minE/349538‑349663

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