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
A5 F1 I1 R1	81	47.9	2225048	94.8%	2109345	113.5

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	92.3%	84.4 / 0.3	26	coding (1262/1455 nt)	xylB	xylulokinase
Reads supporting (aligned to +/- strand): ref base . (0/2); new base C (10/14); total (10/16)
Fisher's exact test for biased strand distribution p-value = 5.08e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATGCACGA  >  NC_000913/3728000‑3728236

cTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAgctgct                                                                                                     <  1:887332/139‑1 (MQ=255)

cTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAgctgct                                                                                                     <  2:437263/139‑1 (MQ=255)

            aCTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGatat                                                                                         >  1:551665/1‑139 (MQ=255)

                ttCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGc                                                                                     <  2:604695/139‑1 (MQ=255)

                          aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGTTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGa                                                                           >  2:618106/1‑139 (MQ=255)

                          aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGTTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTCATATCCGCCAGCATCTGa                                                                           <  1:618106/139‑1 (MQ=255)

                          aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGa                                                                           >  1:149347/1‑139 (MQ=255)

                          aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCCTACGGTAATCGAGCTGCTGACCGCCGATATCCGCCCGCATCTGa                                                                           >  1:947694/1‑139 (MQ=255)

                            ttGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACg                                                                         <  2:551665/139‑1 (MQ=255)

                             tGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGc                                                                        <  2:184116/139‑1 (MQ=255)

                               cGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCa                                                                      <  2:184451/139‑1 (MQ=255)

                               cGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCCGACACCCGCCAGCCTCTGACCCCa                                                                      >  1:458561/1‑139 (MQ=255)

                                        ttCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGC‑TCTAACGCCAGTACTCACTa                                                            >  2:473712/1‑139 (MQ=255)

                                                 cGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGa                                                                                                   >  1:182854/1‑92 (MQ=255)

                                                 cGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGa                                                                                                   <  2:182854/92‑1 (MQ=255)

                                                  gATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑ccccccc                                                                                                                         <  2:973801/68‑1 (MQ=255)

                                                  gATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑ccccccc                                                                                                                         >  1:973801/1‑68 (MQ=255)

                                                          tGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAAt                                           <  2:907057/139‑1 (MQ=255)

                                                          tGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAAt                                           <  2:936091/139‑1 (MQ=255)

                                                          tGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAAt                                           <  1:438736/139‑1 (MQ=255)

                                                                 gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTa                                    >  2:518986/1‑139 (MQ=255)

                                                                        tCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTg                            <  2:428559/139‑1 (MQ=255)

                                                                        tCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTg                            <  2:598542/139‑1 (MQ=255)

                                                                                  ccTTGCTGCGCCCAGTGCTGGTCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGCACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAAt                   >  1:668065/1‑139 (MQ=255)

                                                                                   cTTGCTGCGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATa                  <  2:947694/139‑1 (MQ=255)

                                                                                      gctgcGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCCGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCg               >  2:3025/1‑139 (MQ=255)

                                                                                        tgcGCCCAGTGCTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCa             <  2:149347/139‑1 (MQ=255)

                                                                                                   cTGGCCCCACATCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATGCACGa  <  2:458561/139‑1 (MQ=255)

CTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCACAT‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATGCACGA  >  NC_000913/3728000‑3728236

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A