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	1,051,238	T→C	22.8%	intergenic (+286/+147)	insB → / ← cspH	IS1 transposase InsAB'/stress protein, member of the CspA‑family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,051,238	0	T	C	22.8%	109.0 / 32.4	57	intergenic (+286/+147)	insB/cspH	IS1 transposase InsAB'/stress protein, member of the CspA‑family
Reads supporting (aligned to +/- strand): ref base T (14/30); new base C (6/7); total (20/37)
Fisher's exact test for biased strand distribution p-value = 5.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.89e-01

GAAATTGTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCTTTGTGGAAAAGT  >  W3110S.gb/1051171‑1051306

gAAATTGTTACGAAAGCTATTAATTATTGTTGGTATTATAGTTTCAAGTGGTACTATAACTGGCTGTTa                                                                     <  1:3618312/69‑1 (MQ=255)

gAAATTGTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTa                                                                     <  1:630958/69‑1 (MQ=255)

gAAATTGTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTa                                                                     <  1:2353667/69‑1 (MQ=255)

gAAATTGTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTa                                                                     >  1:2570078/1‑69 (MQ=255)

gAAATTGTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTa                                                                     <  1:69094/69‑1 (MQ=255)

 aaaTTGTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTaa                                                                    <  1:2546905/69‑1 (MQ=255)

 aaaTTGTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTaa                                                                    <  1:2683849/69‑1 (MQ=255)

     tGTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATgg                                                                >  1:1139888/1‑69 (MQ=255)

     tGTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATgg                                                                >  1:2743274/1‑69 (MQ=255)

     tGTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATgg                                                                >  1:1319060/1‑69 (MQ=255)

      gTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGc                                                               >  1:2838705/1‑69 (MQ=255)

            aaaGCTATTAATTATTGTTGTTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTtat                                                         <  1:1889673/69‑1 (MQ=255)

            aaaGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTtat                                                         <  1:1528743/69‑1 (MQ=255)

            aaaGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTtat                                                         <  1:2485602/69‑1 (MQ=255)

            aaaGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTtat                                                         >  1:1836607/1‑69 (MQ=255)

            aaaGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTtat                                                         <  1:3679434/69‑1 (MQ=255)

                   ttaattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTAtt                                                  >  1:625187/1‑69 (MQ=255)

                     aattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTaaa                                                                   <  1:3513156/50‑1 (MQ=255)

                     aattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTaaa                                                                   <  1:2963368/50‑1 (MQ=255)

                     aattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTaaa                                                                   <  1:3397179/50‑1 (MQ=255)

                     aattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTaaa                                                                   <  1:925854/50‑1 (MQ=255)

                     aattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTaaa                                                                   <  1:654001/50‑1 (MQ=255)

                     aattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTaaa                                                                   <  1:1767980/50‑1 (MQ=255)

                     aattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGc                                                               <  1:1071308/54‑1 (MQ=255)

                     aattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAg                                                >  1:3369317/1‑69 (MQ=255)

                     aattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAg                                                >  1:1181379/1‑69 (MQ=255)

                     aattaTTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTtata                                                        >  1:1950584/1‑61 (MQ=255)

                     aattaTTGTTGGTAATATAGTTTCAAGAGGTACTATAACTGGCTGTCAAATGGCATTtata                                                        >  1:1691558/1‑61 (MQ=255)

                        tattGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTg                                             <  1:1229729/69‑1 (MQ=255)

                            gttgGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCag                                          <  1:1839944/68‑1 (MQ=255)

                            gttgGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCag                                          <  1:2753969/68‑1 (MQ=255)

                            gttgGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCag                                          <  1:3287774/68‑1 (MQ=255)

                            gttgGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCag                                          <  1:3292169/68‑1 (MQ=255)

                            gttgGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCa                                           <  1:2750003/67‑1 (MQ=255)

                               ggTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAgaga                                       <  1:2448188/68‑1 (MQ=255)

                               ggTAATATAGTTTCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAgaga                                       <  1:1586625/68‑1 (MQ=255)

                                   atatAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCag                                          >  1:1707686/1‑61 (MQ=255)

                                   atatAGTTTCAAGTGGTACTATAACTGGATGTTAAATGGCATTTATAACTATTAGGTGCag                                          >  1:3546342/1‑61 (MQ=255)

                                     ataGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCAtt                                                            <  1:243874/41‑1 (MQ=255)

                                     ataGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCAtt                                                            <  1:1473070/41‑1 (MQ=255)

                                     ataGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCAtt                                                            <  1:2287272/41‑1 (MQ=255)

                                      taGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTtat                                                         <  1:2641531/43‑1 (MQ=255)

                                      taGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCa                                           <  1:2565627/57‑1 (MQ=255)

                                      taGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCa                                           >  1:2019259/1‑57 (MQ=255)

                                       aGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTtat                                                         <  1:2858924/42‑1 (MQ=255)

                                           tCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTaaa                           >  1:2300077/1‑68 (MQ=255)

                                           tCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTaaa                           >  1:1952668/1‑68 (MQ=255)

                                           tCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTaaa                           >  1:926216/1‑68 (MQ=255)

                                           tCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTa                             <  1:638941/66‑1 (MQ=255)

                                           tCAAGTGGTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTa                             <  1:941473/66‑1 (MQ=255)

                                                 ggTACTATAACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAgaga                                       <  1:2300403/50‑1 (MQ=255)

                                                    aCTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTact                  <  1:6884/68‑3 (MQ=255)

                                                     cTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCAgaga                                       <  1:3484331/46‑1 (MQ=255)

                                                       ataACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCt              >  1:1962385/1‑69 (MQ=255)

                                                       ataACTGGCTGTCAAATGGCATTTATAACTATTAGGTGCaga                                         <  1:1145113/42‑1 (MQ=255)

                                                          aCTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCTTtg           >  1:2211128/1‑69 (MQ=255)

                                                          aCTGGCTGTCAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCTTtg           >  1:1340136/1‑69 (MQ=255)

                                                                   tAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCTTTGTGGAAAAGt  >  1:34692/1‑69 (MQ=255)

GAAATTGTTACGAAAGCTATTAATTATTGTTGGTAATATAGTTTCAAGTGGTACTATAACTGGCTGTTAAATGGCATTTATAACTATTAGGTGCAGAGATATTCGCTTAAATGGATTAGTTTCTTTGTGGAAAAGT  >  W3110S.gb/1051171‑1051306

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A