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	3,013,681	G→A	100%	V11V (GTC→GTT)	yqeC ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	3,013,681	0	G	A	85.5%	155.2 / 19.1	62	V11V (GTC→GTT)	yqeC	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (1/8); new base A (26/27); total (27/35)
Fisher's exact test for biased strand distribution p-value = 6.49e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GCTGGTTTTCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACCTCTCTGGGATAAA  >  W3110S.gb/3013615‑3013740

gcTGGTTTTCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAAc                                                           <  1:258767/69‑1 (MQ=255)

 cTGGTTTTCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACt                                                          <  1:2813441/69‑1 (MQ=255)

 cTGGTTTTCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACt                                                          <  1:2049022/69‑1 (MQ=255)

  tGGTTTTCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACt                                                          <  1:2285902/68‑1 (MQ=255)

  tGGTTTTCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTa                                                         >  1:778892/1‑69 (MQ=255)

       ttCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATggc                                                    >  1:1194733/1‑67 (MQ=255)

       ttCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGcc                                                    >  1:3542144/1‑69 (MQ=255)

          cccccAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGa                                                  <  1:720811/68‑1 (MQ=255)

               aGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGa                                                  <  1:3049141/63‑1 (MQ=255)

               aGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTc                                            <  1:1302389/69‑1 (MQ=255)

                 cACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGcc                                                    >  1:3151474/1‑59 (MQ=255)

                 cACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGcc                                                    >  1:2904349/1‑59 (MQ=255)

                 cACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGcc                                                    >  1:1033557/1‑59 (MQ=255)

                     aacaacAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACtat                                      >  1:2552040/1‑69 (MQ=255)

                     aacaacAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACtat                                      >  1:3192854/1‑69 (MQ=255)

                           aGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAACTATACtttt                                <  1:2266834/69‑1 (MQ=255)

                           aGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAACTATACtttt                                <  1:102384/69‑1 (MQ=255)

                               aTCACAGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGTTGGGTCAACTATACTTTTCACg                            >  1:1283539/1‑69 (MQ=255)

                                 cacaGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACtat                                      >  1:2644586/1‑57 (MQ=255)

                                 cacaGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACtat                                      >  1:3102204/1‑57 (MQ=255)

                                 cacaGTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACtat                                      >  1:3202463/1‑57 (MQ=255)

                                     gTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:3471258/69‑1 (MQ=255)

                                     gTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:1660189/69‑1 (MQ=255)

                                     gTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:2114465/69‑1 (MQ=255)

                                     gTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:3275099/69‑1 (MQ=255)

                                     gTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:1831513/69‑1 (MQ=255)

                                     gTGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:3728066/69‑1 (MQ=255)

                                      tGGGACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCttt                     <  1:791213/69‑1 (MQ=255)

                                        ggACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCttt                     <  1:1619641/67‑1 (MQ=255)

                                        ggACGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCttt                     <  1:946616/67‑1 (MQ=255)

                                          aCGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATg                  <  1:2333935/68‑1 (MQ=255)

                                          aCGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATg                  <  1:2311348/68‑1 (MQ=255)

                                          aCGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATg                  <  1:1269762/68‑1 (MQ=255)

                                          aCGTTTCTGAGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATg                  <  1:2623882/68‑1 (MQ=255)

                                           tgTTTCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAAc                                         <  1:3450899/43‑1 (MQ=255)

                                           cGTTTCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGAc                >  1:1752937/1‑69 (MQ=255)

                                              ttCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACctc             <  1:2536499/69‑1 (MQ=255)

                                               tCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAAc                                         <  1:2487948/40‑1 (MQ=255)

                                               tCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACctc             >  1:1468999/1‑68 (MQ=255)

                                               tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      >  1:3121533/1‑59 (MQ=255)

                                               tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      >  1:3204567/1‑59 (MQ=255)

                                               tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      >  1:3433697/1‑59 (MQ=255)

                                               tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      >  1:1969463/1‑59 (MQ=255)

                                               tCTGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACCAGTCTTTATGACctct            >  1:1012158/1‑69 (MQ=255)

                                                 tGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTAt                   >  1:941464/1‑60 (MQ=255)

                                                 tGCGCACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTAt                   >  1:2570811/1‑60 (MQ=255)

                                                   cgcACCTAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:2644716/55‑1 (MQ=255)

                                                         tAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:2184840/49‑1 (MQ=255)

                                                         tAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:1833111/49‑1 (MQ=255)

                                                         tAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:497703/49‑1 (MQ=255)

                                                         tAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      <  1:2976094/49‑1 (MQ=255)

                                                         tAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACCTCTCTGGGATaaa  <  1:845105/69‑1 (MQ=255)

                                                         tAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACCTCTCTGGGATaa   >  1:2382737/1‑68 (MQ=255)

                                                         tAAATCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACCTCTCTGGGATaa   >  1:1603043/1‑68 (MQ=255)

                                                          aaaTCAATGACTAATGCCGATGGGTCAACTATACtttt                                <  1:3121316/38‑1 (MQ=255)

                                                          aaaTCAATGACTAATGCCGATGGGTCAACTATACtttt                                <  1:2572284/38‑1 (MQ=255)

                                                          aaaTCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCtt                      >  1:783835/1‑48 (MQ=255)

                                                           aaTCAATGACTAATGCCGATGGGTCAACTATACtttt                                <  1:70124/37‑1 (MQ=255)

                                                             tCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTAt                   >  1:2049494/1‑48 (MQ=255)

                                                             tCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTAt                   >  1:2501408/1‑48 (MQ=255)

                                                             tCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTAt                   >  1:981089/1‑48 (MQ=255)

                                                             tCAATAACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACctc             <  1:823587/54‑1 (MQ=255)

GCTGGTTTTCCCCCCAGCACCAACAACAGAAATCACAGTGGGACGTTTCTGCGCACCTAAATCAATGACTAATGCCGATGGGTCAACTATACTTTTCACGAGTCTTTATGACCTCTCTGGGATAAA  >  W3110S.gb/3013615‑3013740

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