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
A13 F1 I2 R1	762	35.5	1545288	95.5%	1475750	117.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,067,224	C→T	intergenic (‑30/+16)	yihP ← / ← yihQ	putative 2,3‑dihydroxypropane‑1‑sulphonate exporter, membrane protein/putative sulpholipid alpha‑glucosidase, alpha‑glucosyl fluoride glucosidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,067,224	0	C	T	100.0%	120.0 / NA	39	intergenic (‑30/+16)	yihP/yihQ	putative 2,3‑dihydroxypropane‑1‑sulphonate exporter, membrane protein/putative sulpholipid alpha‑glucosidase, alpha‑glucosyl fluoride glucosidase
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (23/16); total (23/16)

TATCCAGCAGGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCCCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAACGCTTC  >  NC_000913/4067092‑4067353

tatCCAGCAGGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACggg                                                                                                                             <  2:391552/139‑1 (MQ=255)

  tCCAGCAGGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCg                                                                                                                           >  1:236965/1‑139 (MQ=255)

   ccAGCAGGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCgg                                                                                                                          <  1:182625/139‑1 (MQ=255)

     agcagGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGAt                                                                                                                        <  2:53002/139‑1 (MQ=255)

              ttAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGCGCGGATGTGATTAGa                                                                                                               <  2:515236/139‑1 (MQ=255)

                    gCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCttt                                                                                                         >  2:165093/1‑139 (MQ=255)

                        ggTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTCGATGCTTTTTaa                                                                                                     >  2:614051/1‑139 (MQ=255)

                        ggTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTaa                                                                                                     >  2:266823/1‑139 (MQ=255)

                        ggTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTaa                                                                                                     >  1:564207/1‑139 (MQ=255)

                         gTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGTTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAac                                                                                                    <  1:581312/139‑1 (MQ=255)

                         gTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAac                                                                                                    <  2:236965/139‑1 (MQ=255)

                                    cGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAg                                                                                         >  2:484041/1‑139 (MQ=255)

                                           cagTTTCGCTTTAAAGGGCAGGCGTAAAGTCATTGGATTGGCCGTTGTGATGTGACTCATCGATGTTCACCCTTTGCCCATGAGTTTACTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTgccggc                                                                                  <  2:222159/138‑3 (MQ=255)

                                            actttCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATGTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGCGGTGATCAGATGCTTCTTAACGACGCGAACAGTCCTGccc                                                                                 >  2:681109/3‑139 (MQ=255)

                                              tttCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCAt                                                                               >  2:8349/1‑139 (MQ=255)

                                               ttCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCAtt                                                                              <  1:484041/139‑1 (MQ=255)

                                                                          gCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACggg                                                                                                                             >  2:674567/1‑65 (MQ=255)

                                                                          gCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACggg                                                                                                                             <  1:674567/65‑1 (MQ=255)

                                                                                  ttCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTgc                                                                                      >  2:426691/1‑96 (MQ=255)

                                                                                  ttCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTgc                                                                                      <  1:426691/96‑1 (MQ=255)

                                                                                     cGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATg                                        >  1:69388/1‑139 (MQ=255)

                                                                                          tgatgtgaCTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACggg                                                                                                                             >  1:711097/1‑49 (MQ=255)

                                                                                          tgatgtgaCTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACggg                                                                                                                             <  2:711097/49‑1 (MQ=255)

                                                                                            atgtgaCTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCAt                                 >  2:667930/1‑139 (MQ=255)

                                                                                                   tCATCGATGTTCTCCCTTTGCCCATGAGTTCCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGt                          <  1:266823/139‑1 (MQ=255)

                                                                                                    cATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACggg                                                                                                                             >  1:231636/1‑39 (MQ=255)

                                                                                                    cATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACggg                                                                                                                             <  2:231636/39‑1 (MQ=255)

                                                                                                    cATCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTa                         >  1:275281/1‑139 (MQ=255)

                                                                                                      tCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAAc                       >  2:356964/1‑139 (MQ=255)

                                                                                                      tCGATGTTCTCCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAAc                       >  1:655799/1‑139 (MQ=255)

                                                                                                             tctcCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTccccg                >  1:760244/1‑139 (MQ=255)

                                                                                                               tcCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGaa                                                                                            >  2:51535/1‑61 (MQ=255)

                                                                                                               tcCCTTTGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGaa                                                                                            <  1:51535/61‑1 (MQ=255)

                                                                                                                    ttGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTgccgc                                                                                   <  2:235626/65‑1 (MQ=255)

                                                                                                                    ttGCCCATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTgccgc                                                                                   >  1:235626/1‑65 (MQ=255)

                                                                                                                         cATGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAACGCt    >  2:87997/1‑139 (MQ=255)

                                                                                                                           tGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCAtt                                >  2:561221/1‑109 (MQ=255)

                                                                                                                           tGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCAtt                                <  1:561221/109‑1 (MQ=255)

                                                                                                                           tGAGTTTCCTCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAACGCTTc  >  2:365443/1‑139 (MQ=255)

TATCCAGCAGGATGTTAGAGGCCAGGTCGCCAATACCGTAAGAGAGTTTCTCTTTAAAGGGCAGGCGTAAAGTTGCTGGATCTTCCGTTGTGATGTGACTCATCGATGTTCTCCCTTTGCCCATGAGTTTCCCCACGGGCGGATGTGATTAGATGCTTTTTAACGACGCGAACAGTGCCGCCCATTCGCTATCGGCGCGATAAAAGACCGGCGGCTTGCCGATGGGCGCATTAACGGTAACTTCCCCGCCCCGGAACGCTTC  >  NC_000913/4067092‑4067353

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 16 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A