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
A1 F28 I2 R1	330	0.0	2544031	91.9%	2337964	62.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	4,547,129	G→A	M137I (ATG→ATA)	fimE →	tyrosine recombinase/inversion of on/off regulator of fimA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,547,129	0	G	A	100.0%	141.9 / NA	43	M137I (ATG→ATA)	fimE	tyrosine recombinase/inversion of on/off regulator of fimA
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (41/2); total (41/2)

TATCGCATTATTCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGG  >  W3110S.gb/4547067‑4547190

tATCGCATTATTCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATAtt                                                             <  1:254492/65‑1 (MQ=255)

tATCGCATTATTCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATAtt                                                             <  1:591455/65‑1 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGACCCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:947376/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGCCTCATCCTCATATATTAAGGCATg                                                     >  1:1137403/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCa                                                       >  1:1634042/1‑63 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCAt                                                      >  1:208534/1‑64 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCAt                                                      >  1:1137035/1‑64 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:218339/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:219723/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:2219839/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:2225112/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:2249347/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:2306336/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:23456/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:2347352/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:212815/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:2403699/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:530622/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:2487798/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:110118/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:535196/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:581454/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:64087/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:724400/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:772637/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:848610/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:878198/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:935838/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:949588/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:2012205/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:149103/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:1520852/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:1407091/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:1623665/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:128519/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:1690083/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:1275292/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:1894570/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:1144866/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:1107749/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:1927737/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:194871/1‑65 (MQ=255)

        tattCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATATTAAGGCATg                                                     >  1:2047064/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:1111514/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:835615/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:1313278/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:1040362/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:712902/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:703534/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:667310/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:624041/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:980383/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:1538296/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:1587723/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:29213/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:1592742/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:2499227/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:2459596/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:1676312/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:1701175/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:2325145/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:1900338/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:1901755/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:1903720/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:2189099/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAgg  >  1:1988386/1‑65 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTAGTTTAATTCa    >  1:961874/1‑63 (MQ=255)

                                                           tataTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTCGTGc                      >  1:814262/1‑45 (MQ=255)

TATCGCATTATTCGCGATGCCGGTATTGAAGCTGGAACCGTAACGCAGACTCATCCTCATATGTTAAGGCATGCTTGCGGTTATGAATTGGCGGAGCGTGGTGCAGATACTCGTTTAATTCAGG  >  W3110S.gb/4547067‑4547190

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A