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 F3 I0 R1	560	56.4	4650532	94.9%	4413354	59.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	1,122,815	C→G	29.6%	intergenic (‑283/+4)	yceP ← / ← dinI	hypothetical protein/DNA damage‑inducible protein I

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	1,122,815	0	C	G	29.6%	34.0 / 14.9	27	intergenic (‑283/+4)	yceP/dinI	hypothetical protein/DNA damage‑inducible protein I
Reads supporting (aligned to +/- strand): ref base C (9/10); new base G (5/3); total (14/13)
Fisher's exact test for biased strand distribution p-value = 6.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.21e-01

ATTTTGTACTCAAAATTCGTAAGTAAAATAAAAAAGCCGGGGCGACCCGGCAAAAAAAATCACTGCATATTATTCGCTGACAAACCAGTCATCGGCGCTTTCCCACGTTTCCTGGAGAATTTCACTAATGCGCTG  >  W3110S.gb/1122750‑1122884

aTTTTGTACTCAAAATTCGTAAGTAAAATAAAAAAGCCGGGGCGACCCGGCAAAAAAAATCACTGCatat                                                                   >  1:1783654/1‑70 (MQ=255)

      tACTCAAAATTCGTAAGTAAAATAAAAAAGCCGGGGCGACCCGGCAAAAAAAATCACTGCATATTATTCg                                                             <  1:3760240/70‑1 (MQ=255)

        cTCAAAATTCGTAAGTAAAATAAAAAAGCCGGGGCGACCCGGCAAAAAAAATCACTGCAtatta                                                                 >  1:211727/1‑64 (MQ=255)

         tCAAAATTCGTAAGTAAAATAAAAAAGCCGGGGCGACCCGGCAAAAAAAATCACTGCa                                                                      <  1:4290686/58‑1 (MQ=255)

           aaaaTTCGTAAGTAAAATAAAAAAGCCGGGGCGACCCGGCAAAAAAAATCACTGCATATTATTCGCTGAc                                                        >  1:953273/1‑70 (MQ=255)

              aTTCGTAAGTAAAATAAAAAAGCCGGGGCGACCCGGCAAAAAAAATCACTGCATATTATTCGCTGACAAAc                                                    >  1:1318188/1‑71 (MQ=255)

                        aaaataaaaAAGCCGGGGCGACCCGGCAAAAAAAATCACTGCATATTATTCGCTGACAAACCAGTCATCgg                                          >  1:4634932/1‑71 (MQ=255)

                               gctaaggaagctaaaatggagAAAAAAATCACTGGata                                                                    <  1:535202‑M1/17‑1 (MQ=255)

                                ctaaggaagctaaaatggagAAAAAAATCACTGGatat                                                                   >  1:3742632‑M1/21‑38 (MQ=255)

                                ctaaggaagctaaaatggagAAAAAAATCACTGGatat                                                                   >  1:1678815‑M1/21‑38 (MQ=255)

                                ctaaggaagctaaaatggagAAAAAAATCACTGGata                                                                    >  1:4429769‑M1/21‑37 (MQ=255)

                                 taaggaagctaaaatggagAAAAAAATCACTGGata                                                                    >  1:336797‑M1/20‑36 (MQ=255)

                                  aaggaagctaaaatggagAAAAAAATCACTGGata                                                                    <  1:485887‑M1/17‑1 (MQ=255)

                                  aaggaagctaaaatggagAAAAAAATCACTGGata                                                                    >  1:4098185‑M1/19‑35 (MQ=255)

                                  aaggaagctaaaatggagAAAAAAATCACTGGata                                                                    <  1:2216175‑M1/17‑1 (MQ=255)

                                    ccGGGGCGACCCGGCAAAAAAAATCACTGCATATTATTCGCTGACAAACCAGTCATCGGCGCTTTcc                                  <  1:4089862/67‑1 (MQ=255)

                                    ccGGGGCGACCCGGCAAAAAAAATCACTGCATATTATTCGCTGACAAACCAGTCATCGGCGCTTTc                                   <  1:2769457/66‑1 (MQ=255)

                                     cGGGGCGACCCGGCAAAAAAAATCACTGCATATTATTCGCTGACAAACCAGTCATCGGCGCTTTCCCACGt                             >  1:4335612/1‑71 (MQ=255)

                                       gggCGACCCGGCAAAAAAAATCACTGCATATTATTCGCTGACAAACCAGTCATCGGCGCTTTCCCa                                <  1:4190329/66‑1 (MQ=255)

                                                ggCAAAAAAAATCACTGCATATTATTCGCTGACAAACCAGTc                                               >  1:368316/1‑42 (MQ=255)

                                                 gCAAAAAAAATCACTGCATATTATTCGCTGACaaa                                                     >  1:2434323/1‑35 (MQ=255)

                                                 gCAAAAAAAATCACTGCATATTATTCGCTGACAAACCa                                                  >  1:3318882/1‑38 (MQ=255)

                                                     aaaaaaTCACTGCATATTATTCGCTGACAAACCAGTc                                               <  1:1536488/37‑1 (MQ=255)

                                                      aaaaaTCACTGCATATTATTCGCTGACAAACCAGTCATCGGCGCTTTCCCACGTTTCCTGGAGAATTTCAc            <  1:4233098/71‑1 (MQ=255)

                                                        aaaTCACTGCATATTATTCGCTGACAAACCAGTCATCGGCGCt                                      <  1:3152785/43‑1 (MQ=255)

                                                        aaaTCACTGCATATTATTCGCTGACAAACCAGTCATCGGCGCTTTCCCACGTTTCCTGGAGAATTTCACt           <  1:4314933/70‑1 (MQ=255)

                                                             aCTGCATATTATTCGCTGACAAACCAGTCATCGGCGCTTTCCCACGTTTCCTGgag                    <  1:3499056/56‑1 (MQ=255)

                                                                 cATATTATTCGCTGACAAACCAGTCATCGGCGCTTTCCCACGTTTCCTGGAGAATTTCACTAATGCGCTg  >  1:2004404/1‑70 (MQ=255)

ATTTTGTACTCAAAATTCGTAAGTAAAATAAAAAAGCCGGGGCGACCCGGCAAAAAAAATCACTGCATATTATTCGCTGACAAACCAGTCATCGGCGCTTTCCCACGTTTCCTGGAGAATTTCACTAATGCGCTG  >  W3110S.gb/1122750‑1122884

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