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 R2	316	65.6	5147759	97.4%	5013917	60.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	3,733,360	T→C	42.1%	Y127H (TAC→CAC)	bglB →	cryptic phospho‑beta‑glucosidase B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,733,360	0	T	C	42.1%	24.8 / 72.2	57	Y127H (TAC→CAC)	bglB	cryptic phospho‑beta‑glucosidase B
Reads supporting (aligned to +/- strand): ref base T (18/15); new base C (7/17); total (25/32)
Fisher's exact test for biased strand distribution p-value = 6.57e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.75e-01

TTTTACGATCGGCTGTTTGATGAAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTAATCGAGCGGTCATCGATCACTTC  >  W3110S.gb/3733294‑3733428

ttttACGATCGGCTGTTTGATGAAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGa                                                                  <  1:3351746/71‑1 (MQ=255)

  ttACGATCGGCTGTTTGATGAAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGaaa                                                                >  1:980426/1‑71 (MQ=255)

     cGATCGGCTGTTTGATGAAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGc                                                             <  1:1491733/71‑1 (MQ=255)

       aTCGGCTGTTTGATGAAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCa                                                           <  1:357138/71‑1 (MQ=255)

       aTCGGCTGTTTGATGAAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCa                                                           <  1:1396377/71‑1 (MQ=255)

        tCGGCTGTTTGATGAAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCa                                                           >  1:1292171/1‑70 (MQ=255)

          ggCTGTTTGATGAAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCatat                                                        >  1:2529612/1‑71 (MQ=255)

          ggCTGTTTGATGAAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCatat                                                        >  1:4657288/1‑71 (MQ=255)

              gTTTGATGAAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGcc                                                            <  1:236467/63‑1 (MQ=255)

                ttGATGAAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCATATGGGCTg                                                  >  1:4805294/1‑71 (MQ=255)

                 tgatgaAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGaaa                                                                >  1:1029539/1‑56 (MQ=255)

                 tgatgaAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGaaa                                                                >  1:4265093/1‑56 (MQ=255)

                 tgatgaAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCATATGGGCTgg                                                 >  1:2806170/1‑71 (MQ=255)

                 tgatgaAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCATATGGGCTgg                                                 >  1:1725629/1‑71 (MQ=255)

                 tgatgaAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCATATGGGCTgg                                                 >  1:852095/1‑71 (MQ=255)

                     gaAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTa                                                                     >  1:1116585/1‑47 (MQ=255)

                     gaAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGa                                              >  1:1197942/1‑70 (MQ=255)

                     gaAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGa                                              >  1:13654/1‑70 (MQ=255)

                     gaAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATCACg                                                                   <  1:799796/49‑1 (MQ=255)

                     gaAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCATATGGGCTGGTGa                                              >  1:2927973/1‑70 (MQ=255)

                      aaaTGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGaa                                             <  1:671734/70‑1 (MQ=255)

                      aaaTGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGaa                                             <  1:78186/70‑1 (MQ=255)

                         tGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGa                                                                  <  1:3764160/46‑1 (MQ=255)

                          ggCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGa                                                                  <  1:3632303/45‑1 (MQ=255)

                            cgcAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATCACg                                                                   <  1:744616/42‑1 (MQ=255)

                                 gCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTAcggcgg                                 <  1:227193/71‑1 (MQ=255)

                                 gCGGGGATCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCATATGGGCTGGTGaaa                                            <  1:1203605/60‑1 (MQ=255)

                                 gCGGGGATCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCATATGGGCTGGTGAAAAAc                                         <  1:89774/63‑1 (MQ=255)

                                 gCGGGGATCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCATATGGGCTGGTGAAAAAc                                         <  1:2400370/63‑1 (MQ=255)

                                  cGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGt                                >  1:2267692/1‑71 (MQ=255)

                                  cGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGt                                >  1:478277/1‑71 (MQ=255)

                                    gggATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTg                              <  1:4351255/71‑1 (MQ=255)

                                     ggATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTgg                             >  1:3918598/1‑71 (MQ=255)

                                      gATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTggg                            >  1:3182610/1‑71 (MQ=255)

                                      gATCAAGCCGCTGGTAACGTTATCCCATCACGAAATGc                                                             <  1:1500513/38‑1 (MQ=255)

                                      gATCAAGCCGCTGGTAACGTTATCCCATCACGAAATGc                                                             <  1:4241377/38‑1 (MQ=255)

                                      gATCAAGCCGCTGGTAACGTTATCACATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGtt                               >  1:1093818/1‑68 (MQ=255)

                                       aTCTAGCCGCTGGTTACGTTATCCCATCACGAAATGCCat                                                          <  1:4167217/40‑1 (MQ=25)

                                       aTCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCa                                                           <  1:2636379/39‑1 (MQ=255)

                                       aTCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCat                                                          <  1:4118240/40‑1 (MQ=255)

                                       aTCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCat                                                          <  1:2204762/40‑1 (MQ=255)

                                       aTCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCat                                                          <  1:4820027/40‑1 (MQ=255)

                                       aTCAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCATATGGGCTGGTGaaa                                            <  1:2847059/54‑1 (MQ=255)

                                        tCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCat                                                          <  1:3059610/39‑1 (MQ=255)

                                        tCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGc                           >  1:39062/1‑70 (MQ=255)

                                         cAAGCCTCTGGTAACGTTATCCCATCACGAAATGCCat                                                          <  1:3847488/38‑1 (MQ=38)

                                         cAAGCCGCTGGTAACGTTATCCCATCACGAAATGCCATATGGGCTGGTGAAAAACTAcggcgg                                 >  1:2538039/1‑63 (MQ=255)

                                          aaGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTaa                        >  1:402247/1‑71 (MQ=255)

                                          aaGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTa                         <  1:2820148/70‑1 (MQ=255)

                                               gCTGGTAACGTTATCCCATTACGAATTGCCATATGGGCTGGTGAAAAACTACGGCGGt                                <  1:49250/58‑1 (MQ=255)

                                                        gTTATCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTAc                                      >  1:915589/1‑43 (MQ=255)

                                                         ttATCCCATCACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTAATCGAGCGGTCATc           <  1:2652405/69‑1 (MQ=255)

                                                         ttATCCCATCACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTAATCGAGCGGTCATc           <  1:2706169/69‑1 (MQ=255)

                                                         ttATCCCATCACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTAATCGAGCGGTCATCGa         <  1:1880752/71‑1 (MQ=255)

                                                           aTCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGc                           >  1:4120108/1‑51 (MQ=255)

                                                           aTCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTAATCGAGCGGTCATCGAt        <  1:4609131/70‑1 (MQ=255)

                                                                aTTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTAATCGAGCGGTCATCGATCACTTc  >  1:918917/1‑71 (MQ=255)

                                                                 ttACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTAATCGAGCgg                <  1:3849112/56‑1 (MQ=255)

                                                                 ttACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTAATCGAGCGGTCa             >  1:1607211/1‑59 (MQ=255)

                                                                  tACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTAAt                       >  1:73717/1‑48 (MQ=255)

                                                                  tACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTAATCGAGCGGTCATCg          <  1:512599/61‑1 (MQ=255)

TTTTACGATCGGCTGTTTGATGAAATGGCGCAGGCGGGGATCAAGCCGCTGGTAACGTTATCCCATTACGAAATGCCATATGGGCTGGTGAAAAACTACGGCGGTTGGGCTAATCGAGCGGTCATCGATCACTTC  >  W3110S.gb/3733294‑3733428

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