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	901,754	T→C	49.2%	H533H (CAT→CAC)	ycjM →	predicted glucosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	901,754	0	T	C	49.2%	‑6.0 / 57.5	63	H533H (CAT→CAC)	ycjM	predicted glucosyltransferase
Reads supporting (aligned to +/- strand): ref base T (11/21); new base C (23/8); total (34/29)
Fisher's exact test for biased strand distribution p-value = 2.31e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

AATTGTCTGACTGGATTGTTTAATGTCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACGCTGCGCCCCTGGCAG  >  minE/901689‑901817

gaTTGCCTGACGGGATTGTTTAATGTCAGTGAAAATATTCAGCATATAAATATTACTGACCTGCACGGt                                                              <  1:2767140/68‑1 (MQ=255)

gaTTGCCTGACGGGATTGTTTAATGTCAGTGAAAATATTCAGCATATAAATATTACTGACCTGCACGGt                                                              <  1:2970557/68‑1 (MQ=255)

gaTTGCCTGACGGGATTGTTTAATGTCAGTGAAAATATTCAGCATATAAATATTACTGACCTGCACGGt                                                              <  1:632094/68‑1 (MQ=255)

gaTTGCCTGACGGGATTGTTTAATGTCAGTGAAAATATTCAGCATATAAATATTACTGACCTGCACGGt                                                              <  1:621361/68‑1 (MQ=255)

gaTTGCCTGACGGGATTGTTTAATGTCAGTGAAAATATTCAGCATATAAATATTACTGACCTGCACGGt                                                              <  1:2504374/68‑1 (MQ=255)

gaTTGCCTGACGGGATTGTTTAATGTCAGTGAAAATATTCAGCATATAAATATTACTGACCTGCACGGt                                                              <  1:248278/68‑1 (MQ=255)

gaTTGCCTGACGGGATTGTTTAATGTCAGTGAAAATATTCAGCATATAAATATTACTGACCTGCACGGt                                                              <  1:2355216/68‑1 (MQ=255)

gaTTGCCTGACGGGATTGTTTAATGTCAGTGAAAATATTCAGCATATAAATATTACTGACCTGCACGGt                                                              <  1:3192213/68‑1 (MQ=255)

                tGTTTAATGTCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTg                                              <  1:2238664/69‑1 (MQ=255)

                      aTGTCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGtt                                         <  1:2214911/68‑1 (MQ=255)

                      aTGTCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGtt                                         <  1:2800305/68‑1 (MQ=255)

                      aTGTCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGtt                                         <  1:2361878/68‑1 (MQ=255)

                      aTGTCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGtt                                         <  1:310300/68‑1 (MQ=255)

                      aTGTCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGtt                                         <  1:757945/68‑1 (MQ=255)

                        gTCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:2140810/68‑1 (MQ=255)

                        gTCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:1279660/68‑1 (MQ=255)

                        gTCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:2107999/68‑1 (MQ=255)

                        gTCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:468743/68‑1 (MQ=255)

                         tCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGata                                     <  1:2490092/69‑1 (MQ=255)

                             tAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGATATAtt                                 >  1:2138323/1‑69 (MQ=255)

                             tAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGATATAtt                                 >  1:3374020/1‑69 (MQ=255)

                                  atatTCAGCATGTAAATATTACTAATCTGCATGGTc                                                             >  1:2313648/1‑36 (MQ=255)

                                           aTGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:3093881/49‑1 (MQ=255)

                                           aTGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:2987952/49‑1 (MQ=255)

                                           aTGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:2562351/49‑1 (MQ=255)

                                           aTGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:2515097/49‑1 (MQ=255)

                                           aTGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:2425350/49‑1 (MQ=255)

                                           aTGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:3264944/49‑1 (MQ=255)

                                           aTGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:3120753/49‑1 (MQ=255)

                                           aTGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:310523/49‑1 (MQ=255)

                                              tAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACGc                >  1:3283373/1‑69 (MQ=255)

                                                    ttACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACGCTGCGcc          <  1:934214/69‑1 (MQ=255)

                                                        tAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGa                                       <  1:2211920/36‑1 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATAtt                                 >  1:2691237/3‑40 (MQ=39)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGaaa                      >  1:1527028/3‑51 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:1066125/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:1221955/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:895393/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:793803/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:1447342/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:1607437/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:589573/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:534996/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:165580/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:43712/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:43007/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:1715803/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:3273683/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:17264/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:3229838/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:1753706/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:3157689/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:1951514/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:2153422/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:2283261/3‑69 (MQ=255)

                                                          accTGCACGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACACTGCATCCCTGGc    >  1:2770915/3‑69 (MQ=255)

                                                            cTGCATGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACGCTGCGCCCCTGGCAg  >  1:1663130/1‑69 (MQ=255)

                                                             tGCATGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACGCTGCGcc          >  1:3314990/1‑60 (MQ=255)

                                                             tGCATGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACGCTGCGcc          >  1:40391/1‑60 (MQ=255)

                                                             tGCATGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACGCTGCGCCCCTGGCAg  >  1:425124/1‑68 (MQ=255)

                                                             tGCATGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACGCTGCGCCCCTGGCAg  >  1:2377647/1‑68 (MQ=255)

                                                             tGCATGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACGCTGCGCCCCTGGCAg  >  1:305546/1‑68 (MQ=255)

                                                             tGCATGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACGCTGCGCCCCTGGCAg  >  1:2655209/1‑68 (MQ=255)

AATTGTCTGACTGGATTGTTTAATGTCAGTAAAAATATTCAGCATGTAAATATTACTAATCTGCATGGTCGGGATCTGATTAGTGAAGTTGATATATTGGGTAATGAAATAACGCTGCGCCCCTGGCAG  >  minE/901689‑901817

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