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 F17 I0 R2	276	45.3	3729697	93.0%	3468618	60.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,595,724	G→A	44.4%	pseudogene (56/1401 nt)	ydeU ←	ECK1502:JW1502:b1509; conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,595,724	0	G	A	44.4%	9.7 / 44.4	36	pseudogene (56/1401 nt)	ydeU	ECK1502:JW1502:b1509; conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (7/13); new base A (6/10); total (13/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.70e-01

CTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTG  >  W3110S.gb/1595660‑1595782

cTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGatat                                                         <  1:1617730/68‑1 (MQ=255)

     cGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGtt                                                     <  1:3176825/67‑1 (MQ=255)

     cGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGtt                                                     <  1:1670775/67‑1 (MQ=255)

     cGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGtt                                                     <  1:649244/67‑1 (MQ=255)

     cGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGtt                                                     <  1:1500771/67‑1 (MQ=255)

      ggTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGcc                                                  >  1:407541/1‑69 (MQ=255)

      ggTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGcc                                                  >  1:2246375/1‑69 (MQ=255)

         gggCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGtt                                               <  1:2348574/69‑1 (MQ=255)

               aTTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGt                                         <  1:3344217/69‑1 (MQ=255)

               aTTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGACATTGTTTCCGATATAGTTGCCGTTAACg                                           >  1:3674785/1‑67 (MQ=255)

                ttATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGatat                                                         >  1:2521828/1‑52 (MQ=255)

                ttATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTc                                        <  1:670475/69‑1 (MQ=255)

                ttATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTaa                                             >  1:759346/1‑64 (MQ=255)

                ttATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGta                                        >  1:3136338/1‑68 (MQ=255)

                ttATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTc                                        >  1:2590174/1‑69 (MQ=255)

                ttATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTc                                        <  1:479407/69‑1 (MQ=255)

                ttATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTc                                        <  1:43656/69‑1 (MQ=255)

                ttATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTc                                        >  1:2945526/1‑69 (MQ=255)

                ttATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTc                                        <  1:3080171/69‑1 (MQ=255)

                ttATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTc                                        >  1:3092205/1‑69 (MQ=255)

                 tATCGCCGCCCAGCGTCTCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTc                                        <  1:2257186/68‑1 (MQ=255)

                    cgccgcCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTCAGt                                     <  1:929879/68‑1 (MQ=255)

                    cgccgcCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTCAGt                                     <  1:1475434/68‑1 (MQ=255)

                      ccgccCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGtata                                                        >  1:602579/1‑47 (MQ=255)

                      ccgccCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGtata                                                        >  1:964842/1‑47 (MQ=255)

                      ccgccCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGtata                                                        >  1:316036/1‑47 (MQ=255)

                      ccgccCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTT‑CGGtata                                                        <  1:2052398/46‑1 (MQ=255)

                                                caGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTAt         <  1:2787877/68‑1 (MQ=255)

                                                caGGCCATTGTTTCCGATATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTAt         <  1:1084824/68‑1 (MQ=255)

                                                   gCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCa      <  1:2374423/68‑1 (MQ=255)

                                                   gCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCa      <  1:1078900/68‑1 (MQ=255)

                                                      aTTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTg  <  1:3653196/69‑1 (MQ=255)

                                                      aTTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTg  <  1:810096/69‑1 (MQ=255)

                                                      aTTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTg  <  1:863496/69‑1 (MQ=255)

                                                        tGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACa                                  <  1:2703396/35‑1 (MQ=255)

                                                        tGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACa                                  <  1:2623574/35‑1 (MQ=255)

                                                        tGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGtt                        >  1:250591/1‑45 (MQ=255)

                                                        tGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGtt                        >  1:1902320/1‑45 (MQ=255)

CTTATCGGTGGGCGAATTATCGCCGCCCAGCGTCGCGTTGAACGTCATCAGGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTG  >  W3110S.gb/1595660‑1595782

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