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
A5 F28 I2 R1	721	0.0	1472758	54.8%	807071	56.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	W3110S.gb	2,076,606	T→C	T977T (ACT→ACC)	flu →	antigen 43 (Ag43) phase‑variable biofilm formation autotransporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,076,606	0	T	C	96.5%	298.3 / ‑1.5	114	T977T (ACT→ACC)	flu	antigen 43 (Ag43) phase‑variable biofilm formation autotransporter
Reads supporting (aligned to +/- strand): ref base T (0/4); new base C (110/0); total (110/4)
Fisher's exact test for biased strand distribution p-value = 1.50e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

Only 100 of 114 total aligned reads displayed.

GTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGCACA  >  W3110S.gb/2076562‑2076654

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTTGGGACCTCCACCGCAGGCAGCgg                                 >  1:834026/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCa                                              >  1:1437174/1‑49 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:425099/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:590387/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:918076/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:572472/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:566975/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:559721/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:517022/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:514889/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:501808/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:448389/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:929802/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:650552/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:425030/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:423337/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:422439/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:40602/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:390587/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:930901/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:957993/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:365131/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:344294/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:342726/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:773077/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:884706/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:882442/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:882233/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:880645/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:907354/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:863548/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:84126/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:818142/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:810426/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:802362/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:795027/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:625556/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:732379/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:732104/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:730689/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:720482/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:700385/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:699502/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:696214/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:687546/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:676382/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:325492/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1133937/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1298096/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:974017/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:128134/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1269576/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1265732/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:124645/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1234850/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1217810/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1178545/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1165379/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1138175/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1298557/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1128637/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1118486/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:110897/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:977337/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1091154/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:108137/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1066289/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:106564/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1042152/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1005771/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1454889/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:306682/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:29654/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:294646/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:272977/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:247409/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:240793/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:239461/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:231543/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:211651/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:182274/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1444786/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:144173/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1383690/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1379972/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1360189/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1352503/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:961070/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1328275/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:132200/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCgg                                 >  1:1302978/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCg                                  >  1:1006977/1‑61 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCg                                  >  1:876964/1‑61 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGCAGGCAGCg                                  >  1:1290227/1‑61 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGGACCTCCACCGAAGGCAGCgg                                 >  1:382369/1‑62 (MQ=255)

gTTATCCGCACCTTCAGCTCCCGGGGTGATATGCGTGTGGGAACCTCCACCGCAGGCAGCgg                                 >  1:379719/1‑62 (MQ=255)

                               tGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGcaca  <  1:579852/62‑1 (MQ=255)

                               tGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGcaca  <  1:432057/62‑1 (MQ=255)

                               tGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGcaca  <  1:1102155/62‑1 (MQ=255)

                                  gtgtGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGcaca  <  1:1338805/59‑1 (MQ=255)

GTTATCCGCACCTTCAGCTCCCGGGGAGATATGCGTGTGGGGACTTCCACTGCAGGCAGCGGGATGACGTTCTCTCCCTCACAGAATGGCACA  >  W3110S.gb/2076562‑2076654

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