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 F8 I0 R2	422	46.8	3726540	94.7%	3529033	61.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	2,160,543	C→T	100%	F7F (TTC→TTT)	mdtC →	multidrug efflux system, subunit C

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,160,543	0	C	T	92.6%	72.0 / ‑1.0	27	F7F (TTC→TTT)	mdtC	multidrug efflux system, subunit C
Reads supporting (aligned to +/- strand): ref base C (0/2); new base T (10/15); total (10/17)
Fisher's exact test for biased strand distribution p-value = 5.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

ATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCGGCATA  >  W3110S.gb/2160477‑2160600

aTTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTAttt                                                       <  1:1643462/71‑1 (MQ=255)

          aaaaGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACAGCCCGGt                                             <  1:3071322/71‑1 (MQ=255)

           aaaGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTAt                                                         >  1:3379774/1‑58 (MQ=255)

           aaaGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTAt                                                         >  1:1305416/1‑58 (MQ=255)

           aaaGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTAt                                                         >  1:2713120/1‑58 (MQ=255)

           aaaGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTAt                                                         >  1:2110536/1‑58 (MQ=255)

                  cTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGcgacga                                     <  1:2612335/71‑1 (MQ=255)

                       cccGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGAtttt                                 <  1:1172432/70‑1 (MQ=255)

                       cccGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGAtttt                                 <  1:2761476/70‑1 (MQ=255)

                           tCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCtttattta                                                      <  1:348455/45‑1 (MQ=255)

                           tCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGAtttt                                 <  1:447471/66‑1 (MQ=255)

                           tCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGAtttt                                 <  1:2629742/66‑1 (MQ=255)

                           tCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGAtttt                                 <  1:1782355/66‑1 (MQ=255)

                           tCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGAtttt                                 <  1:3118469/66‑1 (MQ=255)

                            cATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCtttattta                                                      <  1:1972278/44‑1 (MQ=255)

                             aTGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCg                          >  1:2192404/1‑71 (MQ=255)

                             aTGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCg                          >  1:2755659/1‑71 (MQ=255)

                                  gaggagGCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGc                     <  1:2763073/71‑1 (MQ=255)

                                     gaggCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCAt                  <  1:3675304/71‑1 (MQ=255)

                                      aggCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTg                             >  1:3647881/1‑59 (MQ=255)

                                      aggCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCa                   >  1:1842217/1‑69 (MQ=255)

                                      aggCGTAAGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCAt                  <  1:1741249/70‑1 (MQ=255)

                                           tAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTa                <  1:2785536/67‑1 (MQ=255)

                                           tAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTa                <  1:663608/67‑1 (MQ=255)

                                             aGTGAAGTTTTTTGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCtgt          >  1:1000443/1‑71 (MQ=255)

                                                    ttttttGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGcc                    <  1:669708/54‑1 (MQ=255)

                                                    ttttttGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCGGCAt   <  1:1557696/71‑1 (MQ=255)

                                                    ttttttGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCGGCAt   <  1:2500851/71‑1 (MQ=255)

                                                     tttttGCCCTCTTTATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCGGCATa  >  1:643304/1‑71 (MQ=255)

ATTGTGGACCAAAAGCCGCTTTGCCCGTCATGAAGAGGAGGCGTAAGTGAAGTTTTTTGCCCTCTTCATTTACCGCCCGGTGGCGACGATTTTACTGTCGGTTGCCATTACCCTGTGCGGCATA  >  W3110S.gb/2160477‑2160600

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