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
A15 F40 I0 R1	13	14.1	329232	94.7%	311782	135.8

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,279,705	G→A	100%	A943V (GCA→GTA)	ebh_3 ←	Extracellular matrix‑binding protein ebh

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,279,705	0	G	A	100.0%	34.7 / NA	15	A943V (GCA→GTA)	ebh_3	Extracellular matrix‑binding protein ebh
Reads supporting (aligned to +/- strand): ref base G (0/0); new base A (11/4); total (11/4)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATT  >  USA300TCH1516_ALE/2279583‑2279829

ttGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGGTGTGTCGACACAAAAATTGTTATTAGCTTTCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCAcc                                                                                                                 <  1:61001/136‑1 (MQ=255)

    ttCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGtt                                                                                                             >  1:91098/1‑136 (MQ=255)

                        ttACTTCGTTATCCATTGTCGGAATATTTATTAATACATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTgg                                                                                         >  1:6256/1‑136 (MQ=255)

                                 tATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTACGGTTTATCATTTGCATCATCAGTTGATGATGTTACGGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCgg                                                                                >  1:161184/1‑136 (MQ=255)

                                 tATCCATTGTCGGACTGTTTGTTGATACAAATACACAAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCgg                                                                                >  1:118575/1‑136 (MQ=255)

                                      aTTGTCGGACTGTTTGTTGATGCATATACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGTATCATCAATTGCTGATGTTAATGTTGTTTCATTTGTTACCGCATAAATACTAAGTGGTGTGGTGGgagatg                                                                           >  2:121392/1‑134 (MQ=255)

                                                    tgttgCTGCATCTACACTAGAAATGATATTAACTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCa                                                             >  1:72024/1‑136 (MQ=255)

                                                                                ttaGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTATTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTCGGtt                                 >  1:125867/1‑136 (MQ=255)

                                                                                ttaGCTTGCGGTTTATCATTTACATCATCAGTAGCAGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGtt                                 >  1:39541/1‑136 (MQ=255)

                                                                                     ttGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTTTTGCCGCATCCCTATTATTTGGTGTTGTCGGAGCAGCGTCTGCTTTGCCATTAGCTGTCGTCTAAGATCCGGTAGAttcttca                            >  2:94886/1‑131 (MQ=255)

                                                                                      tGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCTGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTTCCATTAGCTGTCGTCTTAGATACGATAGGTTGTCCAg                           <  1:26084/136‑1 (MQ=255)

                                                                                        cGGTTTATCATTTGCATCATCAGTAGCTAATGTTAATGTAGATTCACATGTTGCCGCATAACTATTAATCACTATTATCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTa                         >  1:162448/1‑136 (MQ=255)

                                                                                                 aTTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGgt                <  2:91098/136‑1 (MQ=255)

                                                                                                          atcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTa       <  2:6256/136‑1 (MQ=255)

                                                                                                               ttGCTGCTGTTACTGTTATTTCAAAAATTAACACATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCAtt  >  1:120765/1‑136 (MQ=255)

TTGATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCATTAGCATT  >  USA300TCH1516_ALE/2279583‑2279829

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A