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
A13 F1 I2 R1	762	35.5	1545288	95.5%	1475750	117.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,736,160	+A	intergenic (+3/+193)	xylR → / ← bax	xylose divergent operon transcriptional activator/putative glucosaminidase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,736,159	1	.	A	97.9%	148.9 / ‑5.2	47	intergenic (+2/+194)	xylR/bax	xylose divergent operon transcriptional activator/putative glucosaminidase
Reads supporting (aligned to +/- strand): ref base . (0/0); major base A (22/24); minor base T (1/0); total (23/24)
Fisher's exact test for biased strand distribution p-value = 4.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAGCG‑ATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAG  >  NC_000913/3736022‑3736282

aaCCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACg‑a                                                                                                                            <  2:289401/139‑1 (MQ=255)

  ccaccTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACg‑aat                                                                                                                          >  2:767059/1‑137 (MQ=255)

     ccTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACg‑aatgat                                                                                                                       >  1:246073/1‑134 (MQ=255)

          tCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGaa                                                                                                                   >  1:485373/1‑139 (MQ=255)

            gATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAAtt                                                                                                                 >  2:513835/1‑139 (MQ=255)

                aaTGAGATATCGCAAATGTGGGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGTATGATGAGAATTGTCg                                                                                                             >  1:522882/1‑139 (MQ=255)

                  tGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGc                                                                                                           >  1:612597/1‑139 (MQ=255)

                   gagaTATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCg                                                                                                          <  2:612597/139‑1 (MQ=255)

                        atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTcaca                                                                                                     <  1:177745/139‑1 (MQ=255)

                        atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTcaca                                                                                                     >  1:40363/1‑139 (MQ=255)

                        atCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTcaca                                                                                                     <  1:557918/139‑1 (MQ=255)

                         tCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACAt                                                                                                    >  1:445826/1‑139 (MQ=255)

                          cGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATc                                                                                                   >  2:78693/1‑139 (MQ=255)

                            cAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAg                                                                                                 >  1:248540/1‑139 (MQ=255)

                               aTGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTa                                                                                              >  2:330069/1‑139 (MQ=255)

                                tgtgCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATTATGAGAATTGTCGGCGTCACATCAGGTaa                                                                                             <  2:248540/139‑1 (MQ=255)

                                      gTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGc                                                                                       <  1:230061/139‑1 (MQ=255)

                                       ttATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTTGGCGTCACATCAGGTAACGCTGCg                                                                                      <  2:522882/139‑1 (MQ=255)

                                       ttATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCg                                                                                      <  2:663971/139‑1 (MQ=255)

                                        tATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCAGATCAGGTAACGCTGCGt                                                                                     <  2:441568/139‑1 (MQ=255)

                                                 cTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCgg                                                                            >  1:509004/1‑139 (MQ=255)

                                                   gCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGAt                                                                          <  2:307230/139‑1 (MQ=255)

                                                            cTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGc                                                                                                           <  2:608726/97‑1 (MQ=255)

                                                            cTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGc                                                                                                           >  1:608726/1‑97 (MQ=255)

                                                              aCTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAAc                                                               >  1:246596/1‑139 (MQ=255)

                                                                 ctGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGcc                                                            >  2:722100/1‑139 (MQ=255)

                                                                   gTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCtt                                                          >  2:178951/1‑139 (MQ=255)

                                                                    tttttAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTa                                                         >  2:342737/1‑139 (MQ=255)

                                                                             aaGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTa                                                <  1:240633/139‑1 (MQ=255)

                                                                              aGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTAc                                               >  1:81414/1‑139 (MQ=255)

                                                                                   atGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGcc                                          <  1:767059/139‑1 (MQ=255)

                                                                                   atGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGcc                                          <  1:722100/139‑1 (MQ=255)

                                                                                       cacGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGc                                      <  1:330069/139‑1 (MQ=255)

                                                                                        acgacgCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCa                                     <  2:288100/139‑1 (MQ=255)

                                                                                                aaaaGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGAGGCGGCGTGAACGCCTGATCCGACCTACCCGCCAGGCATGATaaaa                             <  2:445826/139‑1 (MQ=255)

                                                                                                   agagTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGc                          <  2:509004/139‑1 (MQ=255)

                                                                                                    gagTATCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCa                         <  1:78693/139‑1 (MQ=255)

                                                                                                        aTCGCGATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaa                     >  2:265182/1‑139 (MQ=255)

                                                                                                          cgcgATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaaca                   <  1:265182/139‑1 (MQ=255)

                                                                                                          cgcgATGTAAATAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACcaaca                   <  1:178951/139‑1 (MQ=255)

                                                                                                                   aaTAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATaaaa                             <  1:446432/120‑1 (MQ=255)

                                                                                                                   aaTAGCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGATAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATaaaa                             >  2:446432/1‑120 (MQ=38)

                                                                                                                       gCGAGGTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTc      >  2:633332/1‑139 (MQ=255)

                                                                                                                           ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTgg                                                                                   >  1:244186/1‑58 (MQ=255)

                                                                                                                           ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTgg                                                                                   <  2:244186/58‑1 (MQ=255)

                                                                                                                           ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAgg                                       <  1:604031/102‑1 (MQ=255)

                                                                                                                           ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAgg                                       >  2:604031/1‑102 (MQ=255)

                                                                                                                           ggTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAg  >  2:673849/1‑139 (MQ=255)

                                                                                                                            gTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGcg                                                            >  2:466460/1‑79 (MQ=39)

                                                                                                                            gTCATGTTGTAACGAATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGcc                                                            <  1:466460/80‑1 (MQ=39)

AACCACCTTGTCGATCAATGAGATATCGCAAATGTGCGGTTATCCATCGCTGCAATATTTCTACTCTGTTTTTAAAAAAGCATATGACACGACGCCAAAAGAGTATCGCGATGTAAATAGCGAGGTCATGTTGTAGCG‑ATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGTGAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCTCGTAG  >  NC_000913/3736022‑3736282

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `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