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	3,634,018	T→C	11.3%	V46A (GTA→GCA)	yigF →	conserved inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,634,018	0	T	C	11.3%	139.9 / 8.9	53	V46A (GTA→GCA)	yigF	conserved inner membrane protein
Reads supporting (aligned to +/- strand): ref base T (32/15); new base C (4/2); total (36/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAACATGGTTTTCCTGGATTCTGGGGGGCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGATATATTTATTTGTCC  >  W3110S.gb/3633951‑3634086

cAACATGGTTTTCCTGGATTCTGGGGGGCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGt                                                                      <  1:1753491/68‑1 (MQ=255)

    aTGGTTTTCCTGGATTCTGGGGGGCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGAc                                                                 <  1:834152/69‑1 (MQ=255)

      ggTTTTCCTGGATTCTGGGGGGCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACaa                                                               >  1:2298662/1‑69 (MQ=255)

       gTTTTCCTGGATTCTGGGGGGCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGCAAGACAAc                                                              >  1:2268275/1‑69 (MQ=255)

          ttCCTGGATTCTGGGGGGCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGc                                                            >  1:2921087/1‑68 (MQ=255)

          ttCCTGGATTCTGGGGGGCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGc                                                            >  1:1993475/1‑68 (MQ=255)

            ccTGGATTCTGGGGGGCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCtt                                                          <  1:3231769/68‑1 (MQ=255)

               ggATTCTGGGGGGCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACt                                                      >  1:2466079/1‑69 (MQ=255)

                gATTCTGGGGGGCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACt                                                      >  1:221794/1‑68 (MQ=255)

                       gggggCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCa                                                 >  1:2334989/1‑66 (MQ=255)

                           gCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAAt                                          >  1:991948/1‑69 (MQ=255)

                           gCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAAt                                          <  1:3049252/69‑1 (MQ=255)

                           gCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAAt                                          <  1:719094/69‑1 (MQ=255)

                              acacCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAAttt                                        <  1:2492689/68‑1 (MQ=255)

                                acCAGAATATAAAGCAGGATTTAAAGCATTAAAAGTAAGAc                                                                 >  1:2744309/1‑41 (MQ=255)

                                acCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGAc                                                                 >  1:3123903/1‑41 (MQ=255)

                                acCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGAc                                                                 >  1:3448817/1‑41 (MQ=255)

                                acCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCa                                      >  1:1686023/1‑68 (MQ=255)

                                acCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCAt                                     >  1:3094556/1‑69 (MQ=255)

                                 ccAGAATATAAAGCAGCATTTAAAGCATTAAAAGt                                                                      <  1:212360/35‑1 (MQ=255)

                                 ccAGAATATAAAGCAGCATTTAAAGCATTAAAAGt                                                                      <  1:210631/35‑1 (MQ=255)

                                 ccAGAATATAAAGCAGCATTTAAAGCATTAAAAGt                                                                      <  1:1899777/35‑1 (MQ=255)

                                 ccAGAATATAAAGCAGCATTTAAAGCATTAAAAGt                                                                      <  1:3623346/35‑1 (MQ=255)

                                 ccAGAATATAAAGCAGCATTTAAAGCATTAAAAGt                                                                      <  1:1060975/35‑1 (MQ=255)

                                 ccAGAATATAAAGCAGCATTTAAAGCATTAAAAGt                                                                      <  1:87903/35‑1 (MQ=255)

                                 ccAGAATATAAAGCACCATTTAAAGCATTAAAAGt                                                                      <  1:3573424/35‑1 (MQ=255)

                                         taAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTttctt                            >  1:2218215/1‑69 (MQ=255)

                                         taAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTttctt                            >  1:1843903/1‑69 (MQ=255)

                                         taAAGCAGCATTTAAAGCATTAAAAGTAAGACAAAGCTTAACTATTCAAATGAATTTCATTGCTttctt                            >  1:1975673/1‑69 (MQ=255)

                                         taAAGCAGCATTTAAAGCATTAAAAGCAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTttctt                            >  1:524360/1‑69 (MQ=255)

                                           aaGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGc                                  >  1:2433051/1‑61 (MQ=255)

                                           aaGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTttcttc                           <  1:2545359/68‑1 (MQ=255)

                                           aaGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTttcttc                           <  1:2887657/68‑1 (MQ=255)

                                           aaGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTtcttct                          >  1:3038456/1‑69 (MQ=255)

                                            agcagcATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTttcttc                           <  1:3007069/67‑1 (MQ=255)

                                             gcagcaTTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGt                        <  1:2806232/69‑1 (MQ=255)

                                             gcagcaTTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGt                        <  1:2115610/69‑1 (MQ=255)

                                                  aTTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTg                   <  1:2472029/69‑1 (MQ=255)

                                                  aTTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTg                   >  1:1654652/1‑69 (MQ=255)

                                                  aTTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTg                   <  1:2145256/69‑1 (MQ=255)

                                                   tttAAAGCATTAAAAGTAAGACAAGGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTgg                  >  1:1742896/1‑69 (MQ=255)

                                                   tttAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTg                   >  1:945045/1‑68 (MQ=255)

                                                    ttAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGa                 <  1:3423807/69‑1 (MQ=255)

                                                     tAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGa                 >  1:314659/1‑68 (MQ=255)

                                                        aGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGatat              <  1:3488030/68‑1 (MQ=255)

                                                        aGCATTAAAAGCAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGatat              <  1:1553605/68‑1 (MQ=255)

                                                        aGCATTAAAAGCAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGatat              <  1:2605909/68‑1 (MQ=255)

                                                          cATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGATAtatt           <  1:3551455/69‑1 (MQ=255)

                                                              aaaaGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTttcttc                           >  1:414806/1‑49 (MQ=255)

                                                              aaaaGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTc                      >  1:2398735/1‑54 (MQ=255)

                                                              aaaaGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGa                 >  1:3489790/1‑59 (MQ=255)

                                                              aaaaGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGATAtatttatt       >  1:1857385/1‑69 (MQ=255)

                                                              aaaaGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGATAtatttatt       >  1:3359211/1‑69 (MQ=255)

                                                              aaaaGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGATAtatttatt       >  1:1682181/1‑69 (MQ=255)

                                                              aaaaGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGATAtatttatt       >  1:3136767/1‑69 (MQ=255)

                                                              aaaaGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGATAtatttatt       >  1:932798/1‑69 (MQ=255)

                                                              aaaaGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGATAtatttatt       >  1:304178/1‑69 (MQ=255)

                                                              aaaaGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGATAtatttat        >  1:3572987/1‑68 (MQ=255)

                                                              aaaaGCAAGACAACGCTTAACTATTCAAATGAATTTCATTg                                   >  1:1656989/1‑41 (MQ=255)

                                                              aaaaGCAAGACAACGCTTAACTATTCAAATGAATTTCATTGCt                                 >  1:2847713/1‑43 (MQ=255)

                                                                aaGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGATATATTTATTTg     >  1:3140563/1‑69 (MQ=255)

                                                                   tAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGATATATTTATTTGTcc  >  1:2465411/1‑69 (MQ=255)

CAACATGGTTTTCCTGGATTCTGGGGGGCAACACCAGAATATAAAGCAGCATTTAAAGCATTAAAAGTAAGACAACGCTTAACTATTCAAATGAATTTCATTGCTTTCTTCTGTTCCTGGATATATTTATTTGTCC  >  W3110S.gb/3633951‑3634086

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