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
A2 F1 I1 R1	748	32.0	1685426	92.6%	1560704	103.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,240,754	(C)_5→6	coding (915/1041 nt)	galS ←	galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor, mgl operon transcriptional repressor, autorepressor

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,240,749	1	.	C	97.6%	146.4 / ‑3.2	42	coding (920/1041 nt)	galS	galactose‑ and fucose‑inducible galactose regulon transcriptional isorepressor, mgl operon transcriptional repressor, autorepressor
Reads supporting (aligned to +/- strand): ref base . (0/1); new base C (18/23); total (18/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

GAAAGCGGTTACATCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTG‑C‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCGATGATTGAGAGATGTAACGGA  >  NC_000913/2240620‑2240880

gAAAGCGGTTACATCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTCGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTG‑c‑ccccctgc                                                                                                                            <  1:554160/139‑5 (MQ=255)

 aaaGCGGTTACATCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTG‑c‑ccccctgca                                                                                                                           >  2:379915/1‑134 (MQ=255)

            aTCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCg                                                                                                                 <  2:376907/139‑1 (MQ=255)

                         ttgAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCg                                                                                                    >  2:481710/1‑139 (MQ=255)

                          tgAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCg                                                                                                    >  2:449665/1‑138 (MQ=255)

                          tgAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCg                                                                                                    <  1:449665/138‑1 (MQ=255)

                                        ccgccgcATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATgg                                                                                     >  2:610863/1‑139 (MQ=255)

                                        ccgccgcATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATgg                                                                                     >  1:136358/1‑139 (MQ=255)

                                                 tatGGTGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAACACAGTGGCTGGCACGAGGATAAATATTGCCTGGTG‑CGCGGCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGAATAACGCa                                                                            <  2:180995/137‑1 (MQ=255)

                                                 tCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCTTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                            <  2:239142/139‑1 (MQ=255)

                                                 tCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                            <  1:415343/139‑1 (MQ=255)

                                                 tCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                            <  1:379915/139‑1 (MQ=255)

                                                 tCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                            <  2:212969/139‑1 (MQ=255)

                                                          ttGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTa                                                                   >  2:336491/1‑139 (MQ=255)

                                                          ttGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTG‑c‑ccccctgc                                                                                                                            <  1:187518/81‑5 (MQ=255)

                                                          ttGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTG‑c‑ccccctgc                                                                                                                            >  2:187518/1‑77 (MQ=255)

                                                           tGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGcc                                                                                                                       >  2:692359/1‑86 (MQ=255)

                                                           tGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGcc                                                                                                                       <  1:692359/86‑1 (MQ=255)

                                                              gACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTg                                                               <  2:145778/139‑1 (MQ=255)

                                                                  gAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATTAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCggg                                                           >  1:559565/1‑139 (MQ=255)

                                                                    aTGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTc                                                         <  2:3557/139‑1 (MQ=255)

                                                                    aTGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTc                                                         <  1:610863/139‑1 (MQ=255)

                                                                    aTGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTc                                                         <  2:136358/139‑1 (MQ=255)

                                                                          aCGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCg                                                        >  2:808173/1‑134 (MQ=255)

                                                                          aCGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCg                                                        <  1:808173/134‑1 (MQ=255)

                                                                           cGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTaa                                                  <  1:509327/139‑1 (MQ=255)

                                                                             cACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACg                                                >  2:671214/1‑139 (MQ=255)

                                                                                     tCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATgg                                        <  1:336491/139‑1 (MQ=255)

                                                                                          aTAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCg                                                                                                    <  2:557480/74‑1 (MQ=255)

                                                                                          aTAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCg                                                                                                    >  1:557480/1‑74 (MQ=255)

                                                                                            aaaaCAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                            >  2:285476/1‑96 (MQ=255)

                                                                                            aaaaCAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                            <  1:285476/96‑1 (MQ=255)

                                                                                                cAGTGGCTGGCACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCg                             <  1:481710/139‑1 (MQ=255)

                                                                                                   tggctggcACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATCGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGaaa                          >  2:770212/1‑139 (MQ=255)

                                                                                                      ctggcACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCg                       <  2:277187/139‑1 (MQ=255)

                                                                                                        ggcACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCa                                                                                         <  2:710758/71‑1 (MQ=255)

                                                                                                        ggcACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCa                                                                                         >  1:710758/1‑71 (MQ=255)

                                                                                                          cACGAGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCgatga                   >  1:274476/1‑139 (MQ=255)

                                                                                                             gaaacagaaTATTCCCTGCCGCC‑CCCCTGCTAGGCGTGTGCGGTGTATAATTTCGCCATTGAAGCAATGGGATATCGGAAGGTCGTTAATTGAGGGTAGGTGTGACAGGCTATGGGAATATCATGGAAACCGATGATTg                <  2:184042/132‑1 (MQ=255)

                                                                                                              aGGATCAATATTGCCTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCGATGATTga               <  1:671214/139‑1 (MQ=255)

                                                                                                                           ccTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                            <  1:679399/65‑1 (MQ=255)

                                                                                                                           ccTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCa                                                                            >  2:679399/1‑65 (MQ=255)

                                                                                                                           ccTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGgt                                                      >  2:175259/1‑87 (MQ=255)

                                                                                                                           ccTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGgt                                                      <  1:175259/87‑1 (MQ=255)

                                                                                                                           ccTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCga                      >  2:555911/1‑119 (MQ=255)

                                                                                                                           ccTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCga                      <  1:555911/119‑1 (MQ=255)

                                                                                                                           ccTGCTGCC‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCGATGATTGAGAGATGTAACGGa  >  2:185904/1‑139 (MQ=255)

GAAAGCGGTTACATCGCCTGATTTGTTGAGTTAGTGATCGCCGCCGCATTCTGGCGTGTTGCGACAGAATGGCGACGCACTAACGTCGGCATAAAACAGTGGCTGGCACGAGGATCAATATTGCCTGCTG‑C‑CCCCTGCAAGGCCAGTTCGGTGGCTAATTTCGCCATTGAAGCAATGGGATAACGCACGGTCGTTAATTGCGGGTCGGTGTAACGGGCGATGGGAATATCATCGAAACCGATGATTGAGAGATGTAACGGA  >  NC_000913/2240620‑2240880

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 20 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A