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 F21 I0 R1	148	22.8	1772010	97.0%	1718849	61.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,213,568	C→T	52.9%	intergenic (+24/+55)	rpoD → / ← ygjF	RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,213,568	0	C	T	52.9%	‑5.1 / 21.3	17	intergenic (+24/+55)	rpoD/ygjF	RNA polymerase, sigma 70 (sigma D) factor/G/U mismatch‑specific DNA glycosylase
Reads supporting (aligned to +/- strand): ref base C (5/3); new base T (4/5); total (9/8)
Fisher's exact test for biased strand distribution p-value = 6.37e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.58e-01

CCGTTCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGCGTTTTTTATCGCCCACGCAC  >  W3110S.gb/3213508‑3213637

ccGTTCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTACGCCGCACCCg                                                             >  1:184531/1‑71 (MQ=255)

     cTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCgg                                                            <  1:1060672/67‑1 (MQ=255)

     cTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCAc                                                         >  1:482220/1‑70 (MQ=255)

               gcGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCctc                                                >  1:1507895/1‑69 (MQ=255)

                    gCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGcaca                                          <  1:842535/70‑1 (MQ=255)

                            gACGATTAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCAcc                                 >  1:1640759/1‑71 (MQ=255)

                               gATTAATCGGTAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCttt                              <  1:651420/71‑1 (MQ=255)

                                 ttAATCGGTAGGCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACaa                                         <  1:1335181/58‑1 (MQ=255)

                                         tAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCTGTGGCGt                    <  1:241469/71‑1 (MQ=255)

                                            gCCGGATCAGGCGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGCGtttt                 <  1:1113823/71‑1 (MQ=255)

                                                   cAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGCGTTTTTTATCGc          >  1:1309481/1‑71 (MQ=255)

                                                      gCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGCGtttt                 >  1:1634285/1‑61 (MQ=255)

                                                       cGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAAc                                       >  1:663253/1‑38 (MQ=255)

                                                       cGTTATGCCGCACCCGGCACTAGGCCCTCTGCACAAAc                                       >  1:109173/1‑38 (MQ=255)

                                                       cGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGCGTTTTTTATCGCCCAc      <  1:1294459/71‑1 (MQ=255)

                                                         ttATGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTc                            <  1:551632/47‑1 (MQ=255)

                                                           aCGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGCGTTTTTTATCGCCCACGccc  >  1:1476049/1‑69 (MQ=255)

CCGTTCTGAAGTGCTGCGTAGCTTCCTGGACGATTAATCGGTAGGCCGGATCAGGCGTTACGCCGCACCCGGCACTAGGCCCTCTGCACAAACGCCACCTTTTCGGTGGCGTTTTTTATCGCCCACGCAC  >  W3110S.gb/3213508‑3213637

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