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
A3 F50 I2 R1	257	49.9	1554294	99.0%	1538751	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,373,362	T→C	N47N (AAT→AAC)	ycjO →	putative sugar ABC transporter permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,373,362	0	T	C	97.3%	123.9 / ‑4.7	37	N47N (AAT→AAC)	ycjO	putative sugar ABC transporter permease
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (19/17); total (20/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

CGCAATGAACAGGCTTTTTTCAGGTCGTTCCGATATGCCCTTTGCGCTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAATCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGTATACCGCGCTGGTGGTGGCGGGCAGCACCGTGCTCGGGCTGGCGGTGGCG  >  NC_000913/1373218‑1373506

cGCAATGAACAGGCTTTTTTCAGGTCGTTCCGATATGCCCTTTGCGCTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAAc                                                                                                                                            >  2:42441/1‑151 (MQ=255)

   aaTGAACAGGCTTTTTTCAGGTCGTTCCGATATGCCCTTTGCGCTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATc                                                                                                                                         <  1:574125/151‑1 (MQ=255)

          aGGCTTTTTTCAGGTCGTTCCGATATGCCCTTTGCGCTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCa                                                                                                                                   >  2:107073/1‑150 (MQ=255)

           ggCTTTTTTCAGGTCGTTCCGATATGCCCTTTGCGCTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAAc                                                                                                                                 >  2:86467/1‑151 (MQ=255)

                       gTCGTTCCGATATGCCCTTTGCGCTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGt                                                                                                                     <  1:558023/151‑1 (MQ=255)

                         cGTTCCGATATGCCCTTTGCGCTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTg                                                                                                                    <  2:495371/150‑1 (MQ=255)

                               gATATGCCCTTTGCGCTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACt                                                                                                             >  1:355576/1‑151 (MQ=255)

                                    gCCCTTTGCGCTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTAtgt                                                                                                         <  2:11989/150‑1 (MQ=255)

                                          tGCGCTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATc                                                                                                  >  1:639904/1‑151 (MQ=255)

                                           gcgcTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATcc                                                                                                 <  1:744815/151‑1 (MQ=255)

                                            cgcTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCct                                                                                                >  1:46530/1‑151 (MQ=255)

                                               tgctgctTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCCCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCtctc                                                                                             >  1:117946/1‑151 (MQ=255)

                                                       ctcGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCg                                                                                     >  2:358242/1‑151 (MQ=255)

                                                         cgcgCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCgg                                                                                    <  1:240591/150‑1 (MQ=255)

                                                             cccAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCt                                                                               <  1:376985/151‑1 (MQ=255)

                                                             cccAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCt                                                                               >  1:755972/1‑151 (MQ=255)

                                                              ccAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTg                                                                              >  2:375766/1‑151 (MQ=255)

                                                              ccAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTg                                                                              >  2:86298/1‑151 (MQ=255)

                                                                    tattaCTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCAtt                                                                         <  2:52743/150‑1 (MQ=255)

                                                                       taCTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGc                                                                      <  1:86436/150‑1 (MQ=255)

                                                                             tgGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGAt                                                               >  2:165752/1‑151 (MQ=255)

                                                                              gggCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGAt                                                               <  2:175931/150‑1 (MQ=255)

                                                                               ggCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGa                                                             <  2:355622/151‑1 (MQ=255)

                                                                                    tCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTc                                                        >  2:240766/1‑151 (MQ=255)

                                                                                      tggtggCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTg                                                      >  2:548471/1‑151 (MQ=255)

                                                                                       ggtggCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCt                                                       <  1:268532/149‑1 (MQ=255)

                                                                                        gtggcgtggcCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGt                                                    <  2:532810/151‑1 (MQ=255)

                                                                                                                 tCGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGTATACCGCGCTGGTGGTGGCGGgc                             >  1:450703/1‑149 (MQ=255)

                                                                                                                  cGAAATCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGTATACCGCGCTGGTGGTGGCGGgcagc                          >  2:252454/1‑151 (MQ=255)

                                                                                                                      aTCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGTATACCGCGCTGGTGGTGGCGGGCAGCACCg                      <  1:338919/151‑1 (MQ=255)

                                                                                                                       tCAGTTTTTTACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGTATACCGCGCTGGTGGTGGCGGGCAGCAcc                       >  1:34427/1‑149 (MQ=255)

                                                                                                                            tttttACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGTATACCGCGCTGGTGGTGGCGGGCAGCACCGTGCTCg                >  1:192395/1‑151 (MQ=255)

                                                                                                                             ttttACGTCTGCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGTATACCGCGCTGGTGGTGGCGGGCAGCACCGTGCTCg                <  1:374500/150‑1 (MQ=255)

                                                                                                                                       gCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGTATACCGCGCTGGTGGTGGCGGGCAGCACCGTGCTCGGGCTGGCg        <  1:442581/148‑1 (MQ=255)

                                                                                                                                       gCCGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGTATACCGCGCTGGTGGTGGCGGGCAGCACCGTGCTCGGGCTGGCGGTg     <  1:201245/151‑1 (MQ=255)

                                                                                                                                         cGCTCAACCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGTATACCGCGCTGGTGGTGGCGGGCAGCACCGTGCTCGGGCTGGCGGTgg    >  1:754249/1‑150 (MQ=255)

                                                                                                                                            acAATACAAACATCGAGTCAACGTTTGTTGGGGTGAGCAGCTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGTATACCGCGATGGTGGTGGCGGGCAGCAAGGTGCTCGGGCTGGCCGTGGCg  >  1:234600/2‑149 (MQ=255)

CGCAATGAACAGGCTTTTTTCAGGTCGTTCCGATATGCCCTTTGCGCTGCTGCTTCTCGCGCCCAGCTTATTACTGCTGGGCGGTCTGGTGGCGTGGCCGATGGTGTCGAATATCGAAATCAGTTTTTTACGTCTGCCGCTCAATCCCAACATCGAGTCAACGTTTGTTGGGGTGAGCAACTATGTGCGTATCCTCTCCGATCCCGGCTTCTGGCATTCGCTGTGGATGACGGTCTGGTATACCGCGCTGGTGGTGGCGGGCAGCACCGTGCTCGGGCTGGCGGTGGCG  >  NC_000913/1373218‑1373506

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 17 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A