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	2,096,084	G→A	19.3%	E160E (GAG→GAA)	hisB →	fused histidinol‑phosphatase and imidazoleglycerol‑phosphate dehydratase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	W3110S.gb	2,096,084	0	G	A	19.3%	144.0 / 25.8	62	E160E (GAG→GAA)	hisB	fused histidinol‑phosphatase and imidazoleglycerol‑phosphate dehydratase
Reads supporting (aligned to +/- strand): ref base G (28/22); new base A (4/8); total (32/30)
Fisher's exact test for biased strand distribution p-value = 2.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.40e-01

AACATGGGCATTACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTC  >  W3110S.gb/2096022‑2096151

aaCATGGGCATTACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTc                                                               >  1:1428483/1‑69 (MQ=255)

  cATGGGCATTACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTc                                                               >  1:840621/1‑67 (MQ=255)

      ggCATTACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCa                                                                   >  1:2329508/1‑59 (MQ=255)

      ggCATTACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCa                                                                   <  1:3150238/59‑1 (MQ=255)

      ggCATTACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCa                                                                   <  1:3548191/59‑1 (MQ=255)

      ggCATTACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCa                                                                   >  1:162325/1‑59 (MQ=255)

      ggCATTACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCa                                                                   >  1:3074087/1‑59 (MQ=255)

       gCATTACAGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCa                                                                   <  1:120952/58‑1 (MQ=255)

          ttACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTg                                                     <  1:2340598/69‑1 (MQ=255)

          ttACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTg                                                     <  1:2150550/69‑1 (MQ=255)

          ttACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTg                                                     <  1:1833494/69‑1 (MQ=255)

          ttACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTg                                                     <  1:988695/69‑1 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAAGTGGCCAATGATTGGCGAGCAACTCACCAGACGTGAc                                                   >  1:3706655/1‑69 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGAc                                                        >  1:2699003/1‑64 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGt                                                      <  1:1195270/66‑1 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGt                                                      <  1:1881253/66‑1 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGt                                                      <  1:898729/66‑1 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGAc                                                   >  1:3018019/1‑69 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGAc                                                   >  1:2534256/1‑69 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGAc                                                   >  1:513269/1‑69 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGAc                                                   >  1:2482867/1‑69 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGAc                                                   >  1:3398134/1‑69 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGAc                                                   >  1:750810/1‑69 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGAc                                                   >  1:1539838/1‑69 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGAc                                                   >  1:1264304/1‑69 (MQ=255)

            aCTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGAc                                                   >  1:1114117/1‑69 (MQ=255)

               ggTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGt                                                <  1:665283/69‑1 (MQ=255)

               ggTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGt                                                <  1:2510171/69‑1 (MQ=255)

                 tttACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCGTTa                                              >  1:2464941/1‑69 (MQ=255)

                 tttACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCGTTa                                              >  1:1684635/1‑69 (MQ=255)

                     cGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCa                                                           >  1:2056693/1‑52 (MQ=255)

                     cGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCa                                                           >  1:371516/1‑52 (MQ=255)

                     cGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCa                                                           >  1:78331/1‑52 (MQ=255)

                       cTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTc                                         <  1:618780/68‑1 (MQ=255)

                       cTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTc                                         <  1:2729720/68‑1 (MQ=255)

                       cTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTc                                         <  1:1043066/68‑1 (MQ=255)

                        tACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTg                                                     <  1:1826235/55‑1 (MQ=255)

                         aCGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCa                                        >  1:2937874/1‑67 (MQ=255)

                            aCCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACAAGACGTGACCGTTACGCTCACGt                                     <  1:802081/67‑1 (MQ=255)

                                  aaaCCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGt                                                <  1:3671714/50‑1 (MQ=255)

                                  aaaCCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTa                             <  1:3419742/69‑1 (MQ=255)

                                  aaaCCCTGAACTGGCCAATGATTGGCGAACAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTa                             <  1:1165833/69‑1 (MQ=255)

                                  aaaCCCTGAACTGGCCAATGATTGGCGAACAACTCACAAGACGTGACCGTTACGCTCACGTAGTGCGTa                             <  1:2257093/69‑1 (MQ=255)

                                    aCCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGt                                                      <  1:2675000/42‑1 (MQ=255)

                                     cccTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAAt                           >  1:1083151/1‑68 (MQ=255)

                                     cccTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAAt                           >  1:1107233/1‑68 (MQ=255)

                                            cTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAaga                   <  1:3113369/69‑1 (MQ=255)

                                             tGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAaga                   <  1:1894835/68‑1 (MQ=255)

                                                  aaTGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGt                                     <  1:849618/45‑1 (MQ=255)

                                                  aaTGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGt                                     <  1:3515822/45‑1 (MQ=255)

                                                  aaTGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGt                                     <  1:2462610/45‑1 (MQ=255)

                                                  aaTGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGt                                     <  1:796170/45‑1 (MQ=255)

                                                   aTGATTGGCGAACAACTCACCAGACGTGACCGTTACTCTCACGTAGTGCGTa                             <  1:311555/52‑1 (MQ=255)

                                                     gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCAGa           >  1:3661787/1‑68 (MQ=255)

                                                     gATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCAGa           >  1:762286/1‑68 (MQ=255)

                                                      aTTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCAGAtt         >  1:3359848/1‑69 (MQ=255)

                                                      aTTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCAGAtt         >  1:3303430/1‑69 (MQ=255)

                                                      aTTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCAGAtt         >  1:3355525/1‑69 (MQ=255)

                                                      aTTGGCGAGCAACTCACAAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCAGAtt         >  1:606582/1‑69 (MQ=255)

                                                      aTTGGCGAACAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCAGAtt         >  1:749460/1‑69 (MQ=255)

                                                        tgtcGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCAGATTGa       >  1:1192350/4‑69 (MQ=255)

                                                             aGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTc  <  1:248442/69‑1 (MQ=255)

                                                              gCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCAGATTTACGTTc  <  1:474536/68‑1 (MQ=255)

AACATGGGCATTACTGGTTTACGCTACGACCGCGAAACCCTGAACTGGCCAATGATTGGCGAGCAACTCACCAGACGTGACCGTTACGCTCACGTAGTGCGTAATACCAAAGAGACGCAGATTGACGTTC  >  W3110S.gb/2096022‑2096151

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