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 2,961,385 G→A S12S (AGC→AGT)  ppdC ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,961,3850GA99.0% 264.4 / NA 96S12S (AGC→AGT) ppdChypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (95/0);  minor base C (1/0);  total (96/0)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATCACCATCAACACCATCGCCAACATTACCTCCGGCAGGCTAAAGCCTTGTTGATTCTTCA  >  W3110S.gb/2961346‑2961407
                                       |                      
catcaccatcacCACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1044560/1‑62 (MQ=255)
catcaCCATCAACACGATCGCCAAAATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1338280/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGCCTAAAGCCTTGTTGATTCCTCa  >  1:186871/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGAttcctc   >  1:578638/1‑61 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGAttcctc   >  1:796561/1‑61 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGAttcct    >  1:78926/1‑58 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:638183/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:385432/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:624835/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:613846/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:609996/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:602554/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:576278/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:565589/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:554493/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:551375/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:544642/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:541492/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:537468/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:501788/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:478676/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:468430/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:467283/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:441649/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:413882/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:403247/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:997324/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:903170/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:103197/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:9942/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:98742/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:973330/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:97265/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:97164/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:967115/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:949335/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:931644/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:91939/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:647079/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:840396/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:831425/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:823509/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:802674/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:774858/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:755605/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:696291/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:689191/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:663817/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:651361/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1253831/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1410218/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1406589/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1391189/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1364560/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:136335/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1355800/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1335848/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1333757/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1308459/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:126257/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:347639/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1245268/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1233331/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1219577/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:121778/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1181312/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1159073/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:113328/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1129909/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1099084/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1096560/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:26416/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:370531/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:338052/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:325113/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:318696/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:302947/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:299985/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:291747/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:289158/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:279729/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:266768/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1415788/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:260887/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:253500/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:23253/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:230298/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:211667/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:202904/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:18669/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1463550/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1416541/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACCTCCGGCAGACTAAAGCCTAGTTGATTCCTCa  >  1:423428/1‑62 (MQ=255)
catcaCCATCAACACCATCGCCAACATTACATCCGGCAGACTAAAGCCTTGTTGAttcct    >  1:1414872/1‑58 (MQ=255)
catcaCCATCAACACCATCGCCAACAATACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1275123/1‑62 (MQ=255)
catcaCCATCAACAACATCGCCAACATTACCTCCGGCAGACTAAAGCCTTGTTGATTCCTCa  >  1:1212732/1‑62 (MQ=255)
                                       |                      
CATCACCATCAACACCATCGCCAACATTACCTCCGGCAGGCTAAAGCCTTGTTGATTCTTCA  >  W3110S.gb/2961346‑2961407

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