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 I2 R1	764	42.0	2018750	95.5%	1927906	109.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,728,118	(C)_8→9	coding (1254/1455 nt)	xylB ←	xylulokinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,728,110	1	.	C	95.0%	129.4 / ‑0.2	40	coding (1262/1455 nt)	xylB	xylulokinase
Reads supporting (aligned to +/- strand): ref base . (1/1); new base C (17/21); total (18/22)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

AGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑CCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATGCACGACATCCA  >  NC_000913/3727980‑3728242

aGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑ccccc‑cc‑c                                                                                                                              <  1:570338/139‑1 (MQ=255)

  cGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑ccccc‑cc‑ccg                                                                                                                            <  1:925323/139‑3 (MQ=255)

  cGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑ccccc‑cc‑ccg                                                                                                                            >  2:251043/1‑137 (MQ=255)

             tGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑ccccc‑cc‑ccgta                                                                                                                          >  2:232230/1‑126 (MQ=255)

             tGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑ccccc‑cc‑ccgta                                                                                                                          <  1:232230/130‑5 (MQ=255)

               cgcATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCgcg                                                                                                                >  2:548801/1‑137 (MQ=255)

                    cTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCTATTTCTCTGGATTCGCCGCGATCTGCCCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAgctgct                                                                                                           <  1:469352/139‑1 (MQ=255)

                      ggTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGa                                                                                                         <  2:88361/139‑1 (MQ=255)

                         aGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCg                                                                                                      >  2:720893/1‑139 (MQ=255)

                              cGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTCCCGTAGTCGAGCTGCTGGCCGCTGat                                                                                                 >  2:834289/1‑139 (MQ=255)

                                 cTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCCATTTCTCTGGATTCGCTGCGATCTGCGCCAGCCTTACTGCGCCCAGGCCTCGCCCCACAT‑CCCCC‑CCGCCGCCGGCGGTCGAGCTGCTGACCGCTCatacc                                                                                              >  1:665288/1‑137 (MQ=255)

                                              aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGTGCCCAGTGCTGGCCCCACAT‑cccc                                                                                                                                    >  2:220995/1‑89 (MQ=255)

                                              aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGTGCCCAGTGCTGGCCCCACAT‑cccc                                                                                                                                    <  1:220995/89‑1 (MQ=255)

                                              aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGa                                                                                 >  1:853412/1‑139 (MQ=255)

                                              aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCACTGATATCCGCCAGCATCTGa                                                                                 >  2:770264/1‑139 (MQ=255)

                                               gTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑CCCCC‑CC‑CGCACGGTAATCCAGCCCCTGACCGCCGACACCCGCCCGCATCTGACg                                                                               >  1:892007/1‑139 (MQ=255)

                                                       aacaaTTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTAc                                                                        >  1:460427/1‑139 (MQ=255)

                                                         caaTTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTc                                                                      <  2:861860/139‑1 (MQ=255)

                                                             tCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTa                                                                  <  1:720893/139‑1 (MQ=255)

                                                               aaTGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTAcg                                                                <  1:888598/139‑1 (MQ=255)

                                                                    gCGAATTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCTAGTACTCACTACGcgccc                                                           <  2:665288/139‑1 (MQ=255)

                                                                              tGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACTTCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAAt                                                 <  1:251043/139‑1 (MQ=255)

                                                                                   tCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGcgccccgcc                                                       >  1:173304/1‑128 (MQ=255)

                                                                                   tCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGcgccccgcc                                                       <  2:173304/128‑1 (MQ=255)

                                                                                    cgccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑ccccc                                                                                                                                   <  2:156708/52‑1 (MQ=255)

                                                                                    cgccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑ccccc                                                                                                                                   >  1:156708/1‑52 (MQ=255)

                                                                                     gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTa                                          >  1:830318/1‑139 (MQ=255)

                                                                                           aTCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTTACCGCTGATATCCGCCAGCCTCTGACGCCAGTACTCCCTACGCGCCCCCCCCCCAATCAACGTAACACtt                                    >  1:114456/1‑139 (MQ=255)

                                                                                             cTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTg                                  <  2:460427/139‑1 (MQ=255)

                                                                                                    aGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTa                           >  2:219481/1‑139 (MQ=255)

                                                                                                      ccTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTTCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCgg                               >  1:705359/1‑133 (MQ=255)

                                                                                                      ccTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGcc                                                                             <  2:928291/87‑1 (MQ=255)

                                                                                                      ccTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGcc                                                                             >  1:928291/1‑87 (MQ=255)

                                                                                                      ccTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCa                                                   <  2:705832/113‑1 (MQ=255)

                                                                                                      ccTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCa                                                   >  1:705832/1‑113 (MQ=255)

                                                                                                      ccTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCgg                               <  2:705359/133‑1 (MQ=255)

                                                                                                             gcgcCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTg                                  <  2:716379/123‑1 (MQ=255)

                                                                                                             gcgcCCAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCCGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTg                                  >  1:716379/1‑123 (MQ=255)

                                                                                                                cccAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGcgccc                                                           <  2:771083/95‑1 (MQ=255)

                                                                                                                cccAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCa               <  2:830318/139‑1 (MQ=255)

                                                                                                                cccAGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTAATCACTACGcgccc                                                           >  1:771083/1‑95 (MQ=255)

                                                                                                                   aGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACg                                                                               >  2:543078/1‑72 (MQ=255)

                                                                                                                   aGTGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACg                                                                               <  1:543078/72‑1 (MQ=255)

                                                                                                                    gTGCTGTCCCGACAC‑CCCCCGCC‑CGTACGGTAATCGTGCTGCTGACCGCTGATATCCGCCAGCATCTGAAGCCAGTACACACTGCGCGCCCCGCCCCCAATCAACGTAACACTTTGCGATTTAATACCGCAGGCATGCa           <  1:593649/139‑1 (MQ=255)

                                                                                                                    gTGCTGGCCCCACAT‑CCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATGCAc          <  2:892007/139‑1 (MQ=255)

                                                                                                                     tGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCCTCTGACGCCAGTACTc                                                                      >  1:591154/1‑79 (MQ=255)

                                                                                                                     tGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTc                                                                      <  2:591154/79‑1 (MQ=255)

                                                                                                                     tGCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCACTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATGCAc          <  1:770264/139‑1 (MQ=255)

                                                                                                                      gCTGGCCCCACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATGCACg         <  1:827147/139‑1 (MQ=255)

                                                                                                                             ccACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTACCACTTTGCGGTTTAATACCGCAGGCATGCACGACATCCa  <  1:834289/139‑1 (MQ=255)

                                                                                                                             ccACATCCCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATGCACGACATCCa  <  2:853412/139‑1 (MQ=255)

AGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑CCCCC‑CC‑CGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATGCACGACATCCA  >  NC_000913/3727980‑3728242

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A