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
A17 F109 I0 R1	32	27.2	584098	96.5%	563654	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,474,639	C→G	100%	A9129P (GCA→CCA)	ebh ←	extracellular matrix binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,474,639	0	C	G	100.0%	88.7 / NA	26	A9129P (GCA→CCA)	ebh	extracellular matrix binding protein
Reads supporting (aligned to +/- strand): ref base C (0/0); new base G (10/16); total (10/16)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GACCTTTAAATCCATCTTGTTGAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGCTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTACAGTTTGCTCAACGTTAGCATGTTCAT  >  CP000730/1474504‑1474773

gACCTTTAAATCTATCTTGTTGAGTATTGTTTGATGCCTTCAATTGGTCTATGTTATGTTTACCTTTTCTTTTAGCAAGTGCTATACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGa                                                                                                                                    <  2:164/140‑1 (MQ=255)

gACCTTTAAATCCATCTTGTTGAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGa                                                                                                                                    >  2:213952/1‑140 (MQ=255)

                tttttgAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTAt                                                                                                                    <  2:53747/137‑1 (MQ=255)

                   ttgAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCg                                                                                                                 >  2:46129/1‑140 (MQ=255)

                    tgAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGc                                                                                                                <  2:283223/140‑1 (MQ=255)

                     gAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCa                                                                                                               >  1:286808/1‑140 (MQ=255)

                         aTTTTTTAATGCATTCAATTGGTCGATGTCATGTTTTCCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCAtttt                                                                                                           <  1:87540/140‑1 (MQ=255)

                         aTTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCAtttt                                                                                                           <  1:33834/140‑1 (MQ=255)

                           tGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGt                                                                                                         >  2:249354/1‑140 (MQ=255)

                                 aTGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAAt                                                                                                   >  1:78689/1‑140 (MQ=255)

                                   gCATTCAATTGTTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATAc                                                                                                 <  2:198108/140‑1 (MQ=255)

                                      ttCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACAtt                                                                                              <  1:142177/140‑1 (MQ=255)

                                               tCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTtcagcatc                                                                                     <  1:89114/140‑1 (MQ=255)

                                                 gATGTCATGTTTACCATTTTTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTtcagcatcag                                                                                   <  1:101232/140‑1 (MQ=255)

                                                      cATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCAGTTTGTTTCAATACATTTTCAGCATCAGCAATa                                                                              >  2:162636/1‑140 (MQ=255)

                                                                  ttGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATaa                                                                  <  2:167509/140‑1 (MQ=255)

                                                                        tAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCAttt                                                            <  1:46129/140‑1 (MQ=255)

                                                                        tAGCAAGGGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCAttt                                                            <  1:46153/140‑1 (MQ=255)

                                                                         aGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCAtttt                                                           >  2:283248/1‑140 (MQ=255)

                                                                         aGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCAtttt                                                           >  1:56126/1‑140 (MQ=255)

                                                                                                      aTGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCt                              <  1:141411/140‑1 (MQ=255)

                                                                                                          ttGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTACAg                          <  2:111629/140‑1 (MQ=255)

                                                                                                            gTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTTATTTACAGtt                        >  1:288170/1‑140 (MQ=255)

                                                                                                                 gcctttAAGAAATTTTCAAGTAGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTAAAGTTTGCTc                   >  2:98187/4‑140 (MQ=255)

                                                                                                                         aaTATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCTTTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTACTGTTTGCTCAACGTTAg           <  1:145199/140‑1 (MQ=255)

                                                                                                                                  aaGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTACAGTTTGCTCAACGTTAGCATGTTCAt  <  2:286808/140‑1 (MQ=255)

GACCTTTAAATCCATCTTGTTGAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGCTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTACAGTTTGCTCAACGTTAGCATGTTCAT  >  CP000730/1474504‑1474773

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A