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	3,304,430	A→G	24.2%	*415Q (TAA→CAA)	mtr ←	tryptophan transporter of high affinity

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,304,430	0	A	G	24.2%	165.4 / 56.0	91	*415Q (TAA→CAA)	mtr	tryptophan transporter of high affinity
Reads supporting (aligned to +/- strand): ref base A (29/40); new base G (12/10); total (41/50)
Fisher's exact test for biased strand distribution p-value = 3.34e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

GACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGCCGA  >  W3110S.gb/3304362‑3304486

gACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:3146991/71‑1 (MQ=255)

gACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:60693/71‑1 (MQ=255)

gACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:1843484/71‑1 (MQ=255)

gACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:184276/71‑1 (MQ=255)

gACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:615782/71‑1 (MQ=255)

gACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:1759237/71‑1 (MQ=255)

gACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:670658/71‑1 (MQ=255)

gACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:2210216/71‑1 (MQ=255)

gACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:221178/71‑1 (MQ=255)

gACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:3081364/71‑1 (MQ=255)

gACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:231527/71‑1 (MQ=255)

gACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:1105050/71‑1 (MQ=255)

 aCCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACt                                                        <  1:3340363/70‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCTCTGATTACTGATa                                                    <  1:1517921/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:2257296/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:2108136/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:2093779/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:2035293/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:449225/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:474342/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:2654136/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:276043/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:445207/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:1614043/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:891886/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:1489/69‑1 (MQ=255)

      aTAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:672208/69‑1 (MQ=255)

      aTAAGCAAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    <  1:1218249/69‑1 (MQ=255)

        aagcgaagcgCATCAGGCATTGTGTAGGCAGGAGAAATGTCGGATAAGGCACCGCTGATTACTGATaca                                                  >  1:667890/1‑69 (MQ=255)

        aagcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATacac                                                 >  1:2596622/1‑70 (MQ=255)

        aagcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATaca                                                  >  1:1940388/1‑69 (MQ=255)

        aagcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATaca                                                  >  1:2960104/1‑69 (MQ=255)

        aagcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATaca                                                  >  1:3329221/1‑69 (MQ=255)

        aagcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATaca                                                  >  1:1082784/1‑69 (MQ=255)

        aagcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATaca                                                  >  1:212834/1‑69 (MQ=255)

        aagcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATaca                                                  >  1:2919069/1‑69 (MQ=255)

        aagcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACAGCTGATTACTGATaca                                                  >  1:2969724/1‑69 (MQ=255)

         agcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACAcc                                                >  1:2203862/1‑70 (MQ=255)

         agcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACAcc                                                >  1:2752005/1‑70 (MQ=255)

         agcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCg                                               >  1:2921644/1‑71 (MQ=255)

         agcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCg                                               >  1:1647953/1‑71 (MQ=255)

         agcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCg                                               >  1:334121/1‑71 (MQ=255)

         agcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCg                                               >  1:1189545/1‑71 (MQ=255)

         agcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCg                                               >  1:100035/1‑71 (MQ=255)

         agcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCg                                               >  1:3066017/1‑71 (MQ=255)

         agcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCg                                               >  1:2453289/1‑71 (MQ=255)

         agcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCg                                               >  1:2413751/1‑71 (MQ=255)

         agcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCg                                               >  1:441850/1‑71 (MQ=255)

         agcgaagcgCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCg                                               >  1:2387334/1‑71 (MQ=255)

                  cATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATacac                                                 >  1:245449/1‑60 (MQ=255)

                  cATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGGCAGTAAAt                                      >  1:3074744/1‑71 (MQ=255)

                  cATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGGCAGTAAAt                                      >  1:2769399/1‑71 (MQ=255)

                  cATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGGCAGTAAAt                                      >  1:1578555/1‑71 (MQ=255)

                             gtgtAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGa                            >  1:2511764/1‑70 (MQ=255)

                             gtgtAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGa                            >  1:1352781/1‑70 (MQ=255)

                             gtgtAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGa                            >  1:3101613/1‑70 (MQ=255)

                                  ggCAGCTGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCGGCAGTAAATTAAAGCTCGATaaaa                       <  1:1040110/70‑1 (MQ=255)

                                  ggCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCGGCAGTAAATTAAAGCTCGATaaaa                       <  1:2801210/70‑1 (MQ=255)

                                  ggCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCGGCAGTAAATTAAAGCTCGATaaaa                       <  1:2794422/70‑1 (MQ=255)

                                  ggCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCGGCAGTAAATTAAAGCTCGATaaaa                       <  1:3349323/70‑1 (MQ=255)

                                  ggCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCGGCAGTAAATTAAAGCTCGATaaaa                       <  1:2605398/70‑1 (MQ=255)

                                  ggCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCGGCAGTAAATTAAAGCTCGATaaaa                       <  1:2593376/70‑1 (MQ=255)

                                  ggCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCGGCAGTAAATTAAAGCTCGATaaaa                       <  1:2345155/70‑1 (MQ=255)

                                  ggCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCGGCAGTAAATTAAAGCTCGATaaaa                       <  1:2244957/70‑1 (MQ=255)

                                  ggCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCGGCAGTAAATTAAAGCTCGATaaaa                       <  1:1456399/70‑1 (MQ=255)

                                  ggCAGCAGAAATGTCGGATAAGGCACCGCTGATTGCTGATACACCGGCAGTAAATTAAAGCTCGATaaaa                       <  1:758176/70‑1 (MQ=255)

                                   gcagcaGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    >  1:419574/1‑40 (MQ=255)

                                   gcagcaGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    >  1:2590246/1‑40 (MQ=255)

                                   gcagcaGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    >  1:1090556/1‑40 (MQ=255)

                                   gcagcaGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    >  1:2852807/1‑40 (MQ=255)

                                   gcagcaGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    >  1:2570923/1‑40 (MQ=255)

                                   gcagcaGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    >  1:3163009/1‑40 (MQ=255)

                                   gcagcaGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    >  1:1598794/1‑40 (MQ=255)

                                   gcagcaGAAATGTCGGATAAGGCACCGCTGATTACTGATa                                                    >  1:1856445/1‑40 (MQ=255)

                                      gcagAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGTCAGTAAATTAAAGCTCGATaaaa                       <  1:1819519/66‑1 (MQ=255)

                                       cagAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGc                  >  1:3003685/1‑70 (MQ=255)

                                       cagAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGc                  >  1:763168/1‑70 (MQ=255)

                                       cagAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGc                  >  1:2404671/1‑70 (MQ=255)

                                       cagAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGc                  >  1:537999/1‑70 (MQ=255)

                                                   aTAAGGCACCGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATaaaa                       <  1:1226506/53‑1 (MQ=255)

                                                           ccGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGcc    <  1:1927203/64‑1 (MQ=255)

                                                           ccGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGcc    <  1:985403/64‑1 (MQ=255)

                                                           ccGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGcc    <  1:1371291/64‑1 (MQ=255)

                                                           ccGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGcc    <  1:1544541/64‑1 (MQ=255)

                                                           ccGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGcc    <  1:498965/64‑1 (MQ=255)

                                                           ccGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGcc    <  1:461720/64‑1 (MQ=255)

                                                           ccGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGcc    <  1:1974048/64‑1 (MQ=255)

                                                           ccGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGcc    <  1:311731/64‑1 (MQ=255)

                                                           ccGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGcc    <  1:3313650/64‑1 (MQ=255)

                                                             gCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGcc    <  1:2102220/62‑1 (MQ=255)

                                                             gCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGCCGa  >  1:2629445/1‑64 (MQ=255)

GACCTGATAAGCGAAGCGCATCAGGCATTGTGTAGGCAGCAGAAATGTCGGATAAGGCACCGCTGATTACTGATACACCGGCAGTAAATTAAAGCTCGATAAAATATGCACCAGTGCGTTGCCGA  >  W3110S.gb/3304362‑3304486

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