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	2,802,461	G→A	25.0%	A102T (GCC→ACC)	nrdF →	ribonucleoside‑diphosphate reductase 2, beta subunit, ferritin‑like

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,802,461	0	G	A	25.0%	96.0 / 30.3	52	A102T (GCC→ACC)	nrdF	ribonucleoside‑diphosphate reductase 2, beta subunit, ferritin‑like
Reads supporting (aligned to +/- strand): ref base G (21/18); new base A (10/3); total (31/21)
Fisher's exact test for biased strand distribution p-value = 1.98e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGCCTCATGAAGAAGCGGTATTATCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTCGATGCCGCCTACGCC  >  W3110S.gb/2802407‑2802526

aCGCCTCATGAAGAAGCGGTATTATCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAg                                                      <  1:3173137/68‑1 (MQ=255)

          aagaagCGGTATTATCGAATATCAGCTTTATGGAAGCGGTTCATACCCGCTCTTACAGTTCGAtt                                               >  1:3476317/1‑65 (MQ=255)

            gaagCGGTATTATCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTtctc                                          <  1:10963/68‑1 (MQ=255)

            gaagCGGTATTATCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTtctc                                          <  1:1974905/68‑1 (MQ=255)

            gaagCGGTATTATCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTtctc                                          <  1:3578084/68‑1 (MQ=255)

            gaagCGGTATTATCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTtctc                                          <  1:3680856/68‑1 (MQ=255)

                cGGTATTATCGAATATCAGCTTTATGTAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGc                                     <  1:208768/69‑1 (MQ=255)

                 ggTATTATCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCt                                    >  1:178775/1‑69 (MQ=255)

                 ggTATTATCGAATATCAGCTTTATGGAAGCGGTTCATACCCGctct                                                           >  1:3329956/1‑46 (MQ=255)

                 ggTATTATCGAATATCAGCTTTATGGAAGCGGTTCATACCCGctct                                                           >  1:937247/1‑46 (MQ=255)

                     ttatCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACa                                                       >  1:1152980/1‑46 (MQ=255)

                     ttatCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTa                                   >  1:2130056/1‑66 (MQ=255)

                     ttatCGAATATCAGCTTTATGGAAGCGGTTCATACCCGCTCTTACAGTTCGATTTTCTCGACGCTAt                                  >  1:1196593/1‑67 (MQ=255)

                     ttatCGAATATCAGCTTTATGGAAGCGGTTCATACCCGCTCTTACAGTTCGATTTTCTCGACGCTAt                                  >  1:2651639/1‑67 (MQ=255)

                     ttatCGAATATCAGCTTTATGGAAGCGGTTCATACCCGCTCTTACAGTTCGATTTTCTCGACGCTAt                                  >  1:2807462/1‑67 (MQ=255)

                     ttatCGAATATCAGCTTTATGGAAGCGGTTCATACCCGCTCTTACAGTTCGAATTTCTCGACGCTAt                                  >  1:2453392/1‑67 (MQ=255)

                       atCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCa                              >  1:642329/1‑69 (MQ=255)

                       atCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCa                              >  1:3440839/1‑69 (MQ=255)

                       atCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCa                              >  1:81441/1‑69 (MQ=255)

                       atCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCa                              >  1:1514011/1‑69 (MQ=255)

                       atCGAATATCAGCTTTATGGAAGCGGTTCATACCCGCTCTTACAGTTCGATTTtctc                                          <  1:520349/57‑1 (MQ=255)

                       atCGAATATCAGCTTTATGGAAGCGGTTCATACCCGCTCTTACAGTTCGATTTtctc                                          <  1:2434452/57‑1 (MQ=255)

                              atCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCaaa                       <  1:2399954/69‑1 (MQ=255)

                              atCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCaaa                       <  1:721069/69‑1 (MQ=255)

                                 aGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGa                     >  1:2848174/1‑68 (MQ=255)

                                 aGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGAt                    >  1:1002929/1‑69 (MQ=255)

                                 aGCTTTATGGAAGCGGTTCATACCCGCTCTTACAGTTCGATTTTCTCGACGCt                                    >  1:3475750/1‑53 (MQ=255)

                                 aGCTTTATGGAAGCGGTTCATACCCGCTCTTACAGTTCGATTTTCTCGACGCt                                    >  1:1022693/1‑53 (MQ=255)

                                 aGCTTTATGGAAGCGGTTCATACCCGCTCTTACAGTTCGATTTTCTCGACGCt                                    >  1:1810926/1‑53 (MQ=255)

                                   cTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGAtt                                               >  1:1953676/1‑40 (MQ=255)

                                   cTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGAt                                                >  1:3696324/1‑39 (MQ=255)

                                    tttATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTc                 <  1:432038/69‑1 (MQ=255)

                                    tttATGGAAGCGGTTCATACCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTc                 <  1:1951071/69‑1 (MQ=255)

                                     ttATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTc                 <  1:3413315/68‑1 (MQ=255)

                                     ttATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTc                 >  1:3086590/1‑68 (MQ=255)

                                     ttATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTc                 >  1:2209007/1‑68 (MQ=255)

                                     ttATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTc                 <  1:1089421/68‑1 (MQ=255)

                                     ttATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTc                 >  1:431697/1‑68 (MQ=255)

                                     ttATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTc                 >  1:72671/1‑68 (MQ=255)

                                     ttATGGAAGCGGTTCATGCCCGCTCTTACAGTTAGATTTTCTCGACGCTATGCCAGACCAAAGATGTc                 >  1:1336664/1‑68 (MQ=255)

                                        tGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTCGAt              <  1:903122/68‑1 (MQ=255)

                                          gAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCaa                        >  1:312960/1‑56 (MQ=255)

                                          gAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTCGATgcc           >  1:996463/1‑69 (MQ=255)

                                          gAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTCGATgc            >  1:3403310/1‑68 (MQ=255)

                                              cGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGc                                     <  1:479165/39‑1 (MQ=255)

                                                  tCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTCGATGCCGCCTACGc   >  1:3554386/1‑69 (MQ=255)

                                                   cATGGCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCaaa                       <  1:399429/48‑1 (MQ=255)

                                                   cATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCaaa                       <  1:1811210/48‑1 (MQ=255)

                                                   cATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCaaa                       <  1:141347/48‑1 (MQ=255)

                                                   cATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCaaa                       <  1:3336988/48‑1 (MQ=255)

                                                   cATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCaaa                       <  1:999173/48‑1 (MQ=255)

                                                   cATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTCGATGCCGCCTACGcc  >  1:437302/1‑69 (MQ=255)

ACGCCTCATGAAGAAGCGGTATTATCGAATATCAGCTTTATGGAAGCGGTTCATGCCCGCTCTTACAGTTCGATTTTCTCGACGCTATGCCAGACCAAAGATGTCGATGCCGCCTACGCC  >  W3110S.gb/2802407‑2802526

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A