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	349,637	T→G	52.5%	H47Q (CAT→CAG)	hyi →	hydroxypyruvate isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	349,637	0	T	G	52.5%	12.8 / 63.0	61	H47Q (CAT→CAG)	hyi	hydroxypyruvate isomerase
Reads supporting (aligned to +/- strand): ref base T (9/20); new base G (14/18); total (23/38)
Fisher's exact test for biased strand distribution p-value = 4.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.88e-01

GTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGC  >  minE/349579‑349696

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

                              aTGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACa                                   <  1:40326/55‑1 (MQ=255)

                              aTGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACa                                   <  1:1175170/55‑1 (MQ=255)

                              aTGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACa                                   <  1:973799/55‑1 (MQ=255)

                              aTGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACa                                   <  1:2518891/55‑1 (MQ=255)

                              aTGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACa                                   <  1:1727749/55‑1 (MQ=255)

                              aTGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACa                                   <  1:1998599/55‑1 (MQ=255)

                                       aCATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCg                                       <  1:1021752/42‑1 (MQ=255)

                                          ttGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTg         <  1:3149426/69‑1 (MQ=255)

                                           tGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAAttt                    <  1:1305365/57‑1 (MQ=255)

                                           tGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAAttt                    <  1:2939024/57‑1 (MQ=255)

                                           tGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAAttt                    <  1:2639583/57‑1 (MQ=255)

                                           tGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAAttt                    <  1:2604316/57‑1 (MQ=255)

                                           tGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAAttt                    <  1:2364382/57‑1 (MQ=255)

                                           tGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAAttt                    <  1:1799136/57‑1 (MQ=255)

                                           tGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTg         <  1:1505403/68‑1 (MQ=255)

                                            gaagaaTTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGAc       >  1:1996528/1‑69 (MQ=255)

                                            gaagaaTTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGAc       >  1:2253609/1‑69 (MQ=255)

                                            gaagaaTTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGAc       >  1:175792/1‑69 (MQ=255)

                                            gaagaaTTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGAc       >  1:2997212/1‑69 (MQ=255)

                                                 aTTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGggc  >  1:3369796/1‑69 (MQ=255)

GTTTTCGCGGCGTTGAATTTATGTTTCCTTATGACTACGACATTGAAGAATTAAAACATGTGCTGGCGAGTAATAAACTCGAACATACGCTGCACAATTTACCGGCGGGTGACTGGGC  >  minE/349579‑349696

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