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
A13 F20 I0 R1	91	60.0	1338914	94.3%	1262595	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,481,355	G→T	100%	A6890E (GCA→GAA)	ebh ←	extracellular matrix binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,481,355	0	G	T	100.0%	106.7 / NA	35	A6890E (GCA→GAA)	ebh	extracellular matrix binding protein
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (24/11); total (24/11)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TCGCTGTATTCAGTTCCTGAGCGGTTTGAATGGCTTGCGTTACTTCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTGCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGATTAATAATATTTTCAGCA  >  CP000730/1481221‑1481489

ttccTGGATTCAGTTCCTGAGCGGTTTGAATGGCTTGCGTTACTTCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGt                                                                                                                                  <  2:666735/138‑1 (MQ=255)

 cGCTGTATTCAGTTCCTGAGCGGTTTGAATGGCTTGCGTTACTTCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGtt                                                                                                                                 >  1:276235/1‑141 (MQ=255)

     gTATTCAGTTCCTGAGCGGTTTGAATGGCTTGCGTTACTTCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTa                                                                                                                             >  1:109995/1‑141 (MQ=255)

           aGTTCCTGAGCGGTTTGAATGGCTTGCGTTACTGCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCt                                                                                                                       <  2:373710/141‑1 (MQ=255)

            gTTCCTGAGCGGTTTGAATGGCTTGCGTTACTTCAGCTACAGTGTGCGCTTGATGGGTGTTTCCAGTAACAGCACCTTTTTGTGCCTTGTTTAAGTTGTCTGACGTAGATAGTGTTTGGTTTTCATTGTTTTTAGCATCTg                                                                                                                      >  1:555530/1‑141 (MQ=255)

                 tGAGCGGTGTGAATGGCTTGCGTTACTTCAGCTACAGTGTGCGCCTGATCGATATTTCCAGTAACAGCACCCTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTACCATCTGGTACt                                                                                                                 >  2:39802/1‑141 (MQ=255)

                                    gCGTTACTTCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACg                                                                                              <  2:88185/141‑1 (MQ=255)

                                    gCGTTACTTAAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACg                                                                                              <  1:138947/141‑1 (MQ=255)

                                      gTTACTTCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTTGTAGCACCTTTTTGTGCATTGATTTTGACGAGGAACGGGGGTTATCATTGTTTGTCAGTGGTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCt                                                                                            <  1:488692/141‑1 (MQ=255)

                                            tCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTc                                                                                      <  1:578483/141‑1 (MQ=255)

                                            tCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTc                                                                                      >  2:298958/1‑141 (MQ=255)

                                              aGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCACCGCTTGTTTCGt                                                                                    >  1:174424/1‑141 (MQ=255)

                                              aGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGt                                                                                    <  1:109222/141‑1 (MQ=255)

                                               gCTACAGTGTGCGCTAGAATGATGTTTCCAGTAACAGAACCATTTGGATTCTTCTTACATTTATGTGACGTAGCTAATGTTTGGCTTTCATTGTTTTTAGCCTCTGTTACTTTTCTATCACCATTTAACGATTGTTTCGTa                                                                                   >  2:276749/1‑141 (MQ=255)

                                                   cAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTCCTTTTCTATCACCATTCAACGCTTGTTTCGTAgttg                                                                               >  1:169754/1‑141 (MQ=255)

                                                        tgCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTGTATCACCATTAACGGCTGATGTGGTTGTTGTTACa                                                                          >  2:602554/1‑141 (MQ=255)

                                                        tgCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACa                                                                          >  1:368369/1‑141 (MQ=255)

                                                                            aGTAACAGCACCTTTTTGGGCATTGTTTAAGTTATCTAACGTAGATAAGGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAGGTGCTGCTTCAAc                                                      >  2:602783/1‑141 (MQ=255)

                                                                             gTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTCACGTAGTTAAGGGTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACt                                                     <  2:638702/141‑1 (MQ=255)

                                                                             gTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCCATGCCCAACTGGGGTTTCGTAGTTGGTACAGTTGAAAGTGCTGCTTCAACt                                                     >  1:315634/1‑141 (MQ=255)

                                                                               aaCAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTtg                                                   <  1:388388/141‑1 (MQ=255)

                                                                                                       tAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCAtt                           <  1:646542/141‑1 (MQ=255)

                                                                                                       tAAGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCAtt                           >  1:194101/1‑141 (MQ=255)

                                                                                                         aGTTATCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTg                         <  1:551030/141‑1 (MQ=255)

                                                                                                             aTCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACTATTTGCTTg                     >  2:94740/1‑141 (MQ=255)

                                                                                                             aTCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTg                     >  1:590161/1‑141 (MQ=255)

                                                                                                              tCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGa                    >  2:249796/1‑141 (MQ=255)

                                                                                                              tCTAACGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTGGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGGTCGCATTTGTACCATTTGCTTGa                    >  1:101083/1‑141 (MQ=255)

                                                                                                              tCTAACGTAGATAATGTTTGGTTTTCATTGTGTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGa                    >  2:473051/1‑141 (MQ=255)

                                                                                                                   cGTAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTGGTTGTTACAGTTGAAAGTGCTGCTTCAACTTTTGATTGGTTCGCATTTGTACCAGTTTCTTGATtatt               >  2:63269/1‑139 (MQ=255)

                                                                                                                     tAGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGATtaataa             >  2:187698/1‑141 (MQ=255)

                                                                                                                      aGATAATGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGATTaataat            >  1:369067/1‑141 (MQ=255)

                                                                                                                        aTAATGGTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAAGGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCGGCTTCAAATTGCGATTGGTTCGCATTTGTACCATTTGCTTTATTAATAatat          >  2:420176/1‑141 (MQ=255)

                                                                                                                           aTGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGATTAATAATAtttt       >  1:567310/1‑141 (MQ=255)

                                                                                                                           aTGTTTGGTTTTCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGATTAATAATAtttt       >  1:439672/1‑141 (MQ=255)

                                                                                                                             gtttggttttCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTCCCATTTGCTTGATTAATAATATTTTca     >  1:577398/1‑141 (MQ=255)

                                                                                                                                tggttttCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCCTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGATTAATAATATTTtcatca  >  2:556485/1‑141 (MQ=255)

TCGCTGTATTCAGTTCCTGAGCGGTTTGAATGGCTTGCGTTACTTCAGCTACAGTGTGCGCTTGATTGATGTTTCCAGTAACAGCACCTTTTTGTGCATTGTTTAAGTTATCTAACGTAGATAATGTTTGGTTTGCATTGTTTTTAGCATCTGTTACTTTTCTATCACCATTCAACGCTTGTTTCGTAGTTGTTACAGTTGAAAGTGCTGCTTCAACTTGTGATTGGTTCGCATTTGTACCATTTGCTTGATTAATAATATTTTCAGCA  >  CP000730/1481221‑1481489

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A