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 R2	260	44.3	3360226	90.5%	3041004	64.6

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	W3110S.gb	4,154,666	A→G	37.5%	I23V (ATT→GTT)	yhfA →	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	4,154,666	0	A	G	37.5%	50.9 / 66.2	64	I23V (ATT→GTT)	yhfA	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (10/30); new base G (17/7); total (27/37)
Fisher's exact test for biased strand distribution p-value = 5.58e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGCGAGTGAAGTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATGGCGGC  >  W3110S.gb/4154607‑4154730

cgcgAGTGAAGTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGAc                                                       >  1:2416432/1‑71 (MQ=255)

cgcgAGTGAAGTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGAc                                                       >  1:2419510/1‑71 (MQ=255)

cgcgAGTGAAGTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGAc                                                       >  1:2887649/1‑71 (MQ=255)

cgcgAGTGAAGTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGAc                                                       >  1:30792/1‑71 (MQ=255)

          gTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGtttt                                                              <  1:2207063/54‑1 (MQ=255)

          gTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGtttt                                                              <  1:556145/54‑1 (MQ=255)

          gTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGtttt                                                              <  1:1908587/54‑1 (MQ=255)

            gggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTaa                                                            >  1:2401586/1‑54 (MQ=255)

            gggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTaa                                                            >  1:2281591/1‑54 (MQ=255)

            gggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTaa                                                            >  1:2259300/1‑54 (MQ=255)

            gggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTaa                                                            >  1:601070/1‑54 (MQ=255)

            gggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTaa                                                            >  1:2625775/1‑54 (MQ=255)

            gggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTaa                                                            >  1:1817233/1‑54 (MQ=255)

             ggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                           >  1:1826527/1‑70 (MQ=255)

             ggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                           >  1:2244869/1‑70 (MQ=255)

             ggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                           >  1:3329345/1‑70 (MQ=255)

             ggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                           >  1:1642993/1‑70 (MQ=255)

             ggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                           >  1:553749/1‑70 (MQ=255)

             ggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                           >  1:714938/1‑70 (MQ=255)

             ggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                           >  1:74625/1‑70 (MQ=255)

             ggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                           >  1:1438527/1‑70 (MQ=255)

             ggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                           >  1:752259/1‑70 (MQ=255)

             ggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                           >  1:120807/1‑70 (MQ=255)

             ggTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGc                                           >  1:1156303/1‑70 (MQ=255)

                   aGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAg                                    <  1:2948485/71‑1 (MQ=255)

                       ttAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCAcc                                <  1:3083837/71‑1 (MQ=255)

                       ttAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCAcc                                <  1:1801350/71‑1 (MQ=255)

                                   ggCGAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGa                    <  1:2038212/71‑1 (MQ=255)

                                   ggCGAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGa                    <  1:2550077/71‑1 (MQ=255)

                                   ggCGAATCCGCCTCTGGTCATAAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTGCGATGGa                    <  1:1157253/71‑1 (MQ=255)

                                      gAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGaaa                  >  1:1921979/1‑70 (MQ=255)

                                      gAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAAt                 >  1:2089828/1‑71 (MQ=255)

                                      gAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAAt                 >  1:2016892/1‑71 (MQ=255)

                                      gAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAAt                 >  1:3124171/1‑71 (MQ=255)

                                      gAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAAt                 >  1:1999952/1‑71 (MQ=255)

                                      gAATCCGCCTATGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAAt                 >  1:2800138/1‑71 (MQ=255)

                                            gCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:807349/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:592274/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:1574116/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGGTTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:2830776/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATTGAAATGGTGtt           <  1:712972/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:1598904/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:976678/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:1580612/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:580859/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:635652/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:1565848/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:1479952/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:125847/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:899173/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:2336321/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:527272/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:178963/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:1900231/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:2822413/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:2803911/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:2754449/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:2729882/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:2667578/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:2142768/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:2165540/71‑1 (MQ=255)

                                            gCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGtt           <  1:2309910/71‑1 (MQ=255)

                                             ccTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGGACCAAGTCCGATGGAAATGGTGtt           <  1:50512/70‑1 (MQ=255)

                                                      atcaGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATggcggc  <  1:1810786/70‑1 (MQ=255)

CGCGAGTGAAGTGGGTCGAAGGGTTAACTTTTCTGGGCGAATCCGCCTCTGGTCATCAGATTTTAATGGACGGCAACTCAGGCGATAAAGCACCAAGTCCGATGGAAATGGTGTTGATGGCGGC  >  W3110S.gb/4154607‑4154730

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A