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
A6 F1 I2 R1	758	59.3	2864096	93.9%	2689386	105.7

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%	120.9 / NA	38	intergenic (+7/‑50)	allB/ybbY	allantoinase/putative uracil/xanthine transporter
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (20/18); total (20/18)

GTACCATTGGCGCGCGTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTATTTTTTGCAACAC  >  NC_000913/540393‑540638

gTACCATTGGCGCGCGTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTcc                                                                                                             >  1:798839/1‑139 (MQ=255)

              cgTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCAtt                                                                                               >  1:1197429/1‑139 (MQ=255)

              cgTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCAtt                                                                                               >  1:249512/1‑139 (MQ=255)

                 aTCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATtctc                                                                                            <  2:1416822/139‑1 (MQ=255)

                    aCGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCgg                                                                                         <  2:11649/139‑1 (MQ=255)

                       aaaaCCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTa                                                                                      <  2:1079094/139‑1 (MQ=255)

                       aaaaCCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTa                                                                                      <  1:549243/139‑1 (MQ=255)

                               cTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGgtgtgt                                                                              <  2:798839/139‑1 (MQ=255)

                                     tggtgATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTgcgg                                                                                                       <  1:1001137/108‑1 (MQ=255)

                                     tggtgATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTgcgg                                                                                                       >  2:1001137/1‑108 (MQ=255)

                                          atgtgatTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGcc                                                                                                                  <  1:357463/92‑1 (MQ=255)

                                          atgtgatTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGcc                                                                                                                  >  2:357463/1‑92 (MQ=255)

                                          atgtgatTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCg                                                                                                                >  2:292481/1‑94 (MQ=255)

                                          atgtgatTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCg                                                                                                                <  1:292481/94‑1 (MQ=255)

                                                    cGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATtctc                                                                                            <  2:157761/104‑1 (MQ=255)

                                                    cGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATtctc                                                                                            >  1:157761/1‑104 (MQ=255)

                                                            aaCAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAg                                                        >  1:962906/1‑132 (MQ=255)

                                                            aaCAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAg                                                        <  2:962906/132‑1 (MQ=255)

                                                                 ggCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGc                                              <  2:301653/137‑1 (MQ=255)

                                                                 ggCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGc                                              >  1:301653/1‑137 (MQ=255)

                                                                   cTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCg                                                                                          >  1:1182794/1‑91 (MQ=255)

                                                                   cTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCg                                                                                          <  2:1182794/91‑1 (MQ=255)

                                                                      cccTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGt                                                           >  2:383458/1‑119 (MQ=255)

                                                                      cccTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGt                                                           <  1:383458/119‑1 (MQ=255)

                                                                      cccTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTAt                                       >  1:498479/1‑139 (MQ=255)

                                                                           ttGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGcc                                                                                                                  >  1:1090113/1‑59 (MQ=255)

                                                                           ttGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGcc                                                                                                                  <  2:1090113/59‑1 (MQ=255)

                                                                           ttGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAg                                    <  2:877606/137‑1 (MQ=255)

                                                                           ttGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAg                                    >  1:877606/1‑137 (MQ=255)

                                                                                ccGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATtctc                                                                                            <  1:847784/76‑1 (MQ=255)

                                                                                ccGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATtctc                                                                                            >  2:847784/1‑76 (MQ=255)

                                                                                ccGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCa                             >  1:790352/1‑139 (MQ=255)

                                                                                   aaaGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTg                          >  2:787986/1‑139 (MQ=255)

                                                                                               aTCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGtt                       >  2:1248413/1‑130 (MQ=255)

                                                                                               aTCCTTAAACATCAGCAGTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGtt                       <  1:1248413/130‑1 (MQ=255)

                                                                                                           cagcagTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTATTTTTTGCAacac  >  1:712468/1‑139 (MQ=255)

                                                                                                             gcagTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTAttttt          >  1:837014/1‑129 (MQ=255)

                                                                                                             gcagTAATCTGGCTCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTAttttt          <  2:837014/129‑1 (MQ=255)

GTACCATTGGCGCGCGTATCACGAAAACCATCTTACGTGGTGATGTGATTTACGACATTGAACAGGGCTTCCCTGTTGCGCCGAAAGGTCAATTTATCCTTAAACATCAGCAGTAATCTGGCCCCTGCAATGCCCGTCCTTGCGGCGGGCATTCTCCGGTTAAGGTGTGTTTATGTTCAATTTTGCAGTCAGCCGCGAAAGCCTGTTATCAGGATTTCAGTGGTTTTTCTTTATTTTTTGCAACAC  >  NC_000913/540393‑540638

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `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