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
A4 F1 I1 R1	765	39.6	1867486	94.4%	1762906	108.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	540,515	C→T	intergenic (+7/‑50)	allB → / → ybbY	allantoinase/putative uracil/xanthine transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	540,515	0	C	T	100.0%	103.2 / NA	33	intergenic (+7/‑50)	allB/ybbY	allantoinase/putative uracil/xanthine transporter
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (17/16); total (17/16)

CGCGTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTATTTTTTGCAACAC  >  NC_000913/540405‑540638

cgcgTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGcc                                                                                                                  <  2:86306/122‑1 (MQ=255)

cgcgTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGcc                                                                                                                  >  1:86306/1‑122 (MQ=255)

cgcgTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCa                                                                                                 >  1:848040/1‑139 (MQ=255)

     aTCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATtctc                                                                                            <  2:677188/139‑1 (MQ=255)

          gAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGtt                                                                                       <  2:734266/139‑1 (MQ=255)

           aaaaCCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTa                                                                                      <  2:848040/139‑1 (MQ=255)

                        gtggtgATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATg                                                                         >  1:844882/1‑139 (MQ=255)

                          ggtgATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGtt                                                                       <  2:844882/139‑1 (MQ=255)

                             gatgtgatTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCaa                                                                    >  1:116357/1‑139 (MQ=255)

                                 tgatTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAAtttt                                                                >  1:338175/1‑139 (MQ=255)

                                                aaCAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGaa                                                 >  1:825184/1‑139 (MQ=255)

                                                  cAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCa                                                                                                 <  2:735758/89‑1 (MQ=255)

                                                  cAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCa                                                                                                 >  1:735758/1‑89 (MQ=255)

                                                     ggCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCt                                            >  2:330009/1‑139 (MQ=255)

                                                       cTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGt                                          >  2:716692/1‑139 (MQ=255)

                                                          cccTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGc                                                                                                  <  2:242172/80‑1 (MQ=255)

                                                          cccTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGc                                                                                                  >  1:242172/1‑80 (MQ=255)

                                                          cccTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTa                                                                                      >  1:422965/1‑92 (MQ=255)

                                                          cccTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTa                                                                                      <  2:422965/92‑1 (MQ=255)

                                                          cccTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTAt                                       >  2:831358/1‑139 (MQ=255)

                                                                tGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGAt                                 >  1:705282/1‑139 (MQ=255)

                                                                   gcCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTc                              <  2:705282/139‑1 (MQ=255)

                                                                          ggTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGtt                       <  1:716692/139‑1 (MQ=255)

                                                                               aTTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCt                  <  1:817927/139‑1 (MQ=255)

                                                                                      cTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGtt                                                                                       >  2:626404/1‑63 (MQ=255)

                                                                                      cTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGtt                                                                                       <  1:626404/63‑1 (MQ=255)

                                                                                      cTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTAtttt           <  2:383999/139‑1 (MQ=255)

                                                                                        tAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGaa                                                 <  2:516809/99‑1 (MQ=255)

                                                                                        tAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGaa                                                 >  1:516809/1‑99 (MQ=255)

                                                                                          aaCATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTATTTTTTGc       >  1:405556/1‑139 (MQ=255)

                                                                                               cagcagTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCa                                                                                                 >  2:535807/1‑44 (MQ=255)

                                                                                               cagcagTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCa                                                                                                 <  1:535807/44‑1 (MQ=255)

                                                                                               cagcagTAATCTGGCTCCTGCAATACCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGGGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTATTTTTTGCAacac  <  2:510061/139‑1 (MQ=255)

CGCGTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTATTTTTTGCAACAC  >  NC_000913/540405‑540638

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A