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
A1 F169 I1 R1	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,499,376	C→A	G883V (GGT→GTT)	ebh_1 ←	Extracellular matrix‑binding protein ebh

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,499,376	0	C	A	100.0%	96.6 / NA	29	G883V (GGT→GTT)	ebh_1	Extracellular matrix‑binding protein ebh
Reads supporting (aligned to +/- strand): ref base C (0/0); new base A (11/18); total (11/18)

CGCCTCGATAGTATTTGGCATTTATTCCAACAGGATTATTGATTGTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTACCTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTCGCAAGTATCGTATAACCAGATGGTATTTGATCTGCCTCACTACCACCATTCGTAGTTTGATTTGT  >  USA300TCH1516_ALE/1499239‑1499518

cgCCTCGATAGTATTTGGCATTTATTCCAACAGGATTATTGATTGTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAggtgg                                                                                                                                      <  3:16227/148‑1 (MQ=255)

 gCCTCGATAGTATTTGGCATTTATTCCAAGAGGATTATTGATTGTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAAGTTGTTTAACTAc                                                                                                                                            <  2:52142/141‑1 (MQ=255)

 gCCTCGATAGTATTTGGCATTTATTCCAACAGGATTATTGATTGTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAggtggt                                                                                                                                     <  4:387730/148‑1 (MQ=255)

 gCCTCGATAGTATTTGGCATTTATTCCAACAGGATTATTGATTGTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAggtggt                                                                                                                                     <  3:9400/148‑1 (MQ=255)

         aGTATTTGGCATTTATTCCAACAGGATTATTGATTGTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATac                                                                                                                             <  3:42659/148‑1 (MQ=255)

                 gCATTTATTCCAACAGGATTATTGATTGTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAAt                                                                                                                     <  4:383380/148‑1 (MQ=255)

                 gCATTTATTCCAACAGGATTATTGATTGTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAAt                                                                                                                     <  4:348233/148‑1 (MQ=255)

                   aTTTATTCCAACAGGATTATTGATTGTTGGTGGAATGTCATCTGGAAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATacaac                                                                                                                          <  2:65672/141‑1 (MQ=255)

                            aaCAGGATTATTGATTGTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGt                                                                                                          >  4:111650/1‑148 (MQ=255)

                            aaCAGGATTATTGATTGTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGt                                                                                                          >  4:13954/1‑148 (MQ=255)

                            aaCAGGATTATTGATTGTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATGAGATTCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATATTGCGGTCGt                                                                                                          >  4:248479/1‑148 (MQ=255)

                                     attgattgTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAAtt                                                                                                 <  3:406941/148‑1 (MQ=255)

                                     attgattgTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAAtt                                                                                                 <  4:172355/148‑1 (MQ=255)

                                     attgattgTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAAtt                                                                                                 <  4:197608/148‑1 (MQ=255)

                                                     aTGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCAt                                                                                 >  4:203436/1‑148 (MQ=255)

                                                         cATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAgg                                                                             <  4:291739/148‑1 (MQ=255)

                                                            cTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGgtgt                                                                          >  3:271912/1‑148 (MQ=255)

                                                                   aaTAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTc                                                                   <  4:360794/148‑1 (MQ=255)

                                                                     tAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTCGc                                                                 <  3:279623/148‑1 (MQ=255)

                                                                     tAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTCGc                                                                 <  3:71864/148‑1 (MQ=255)

                                                                     tAGTAACAGCATTACTCATATTAGACGCACCTACTTTATTATAATAAACTACCGCTCTAGTTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTCGc                                                                 <  3:392436/148‑1 (MQ=255)

                                                                                        atTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTCGCAAGTATCGTATAACCAGAt                                              >  4:110226/1‑148 (MQ=255)

                                                                                        atTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTCGCAAGTATCGTATAACCAGAt                                              >  3:170996/1‑148 (MQ=255)

                                                                                               gCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTCGCAAGTATCGTATAACCAGATGGTAttt                                       >  4:155150/1‑148 (MQ=255)

                                                                                               gCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTCGCAAGTATCGTATAACCAGATGGTAttt                                       >  4:94820/1‑148 (MQ=255)

                                                                                                                     ctactGCTCTAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTCGCAAGTATCGTATAACCAGATGGTATTTGATCTGCCTCACTACCACCAtt                 <  3:256707/148‑1 (MQ=255)

                                                                                                                             ctAATTTGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTCGCAAGTATCGTATAACCAGATGGTATTTGATCTGCCTCACTACCACCATTCGTAGttt         <  3:124391/148‑1 (MQ=255)

                                                                                                                                  ttGTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGCGTACCAGTCGCAAGTATCGTATAACCAGATGGTATTTGATCTGCCTCACTACCACCATTCGTAGTTTGAttt    >  4:258100/1‑148 (MQ=255)

                                                                                                                                    gTTTAACTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTCGCAAGTATCGTATAACCAGATGGTATTTGATCTGCCTCACTACCACCATTCGTAGTTTGATttgt  >  3:364136/1‑148 (MQ=255)

CGCCTCGATAGTATTTGGCATTTATTCCAACAGGATTATTGATTGTTGGTGGAATGTCATCTGGCAAAATAGTAACAGCATTACTCATATTAGATGCAACTACTTTATTATAATAAACTACTGCTCTAATTTGTTTACCTACAGGTGGTATGAATACAACATAATCTTGCGGTCGTATAGTAATTGTATTATGCACCCCATCAGGTGTACCAGTCGCAAGTATCGTATAACCAGATGGTATTTGATCTGCCTCACTACCACCATTCGTAGTTTGATTTGT  >  USA300TCH1516_ALE/1499239‑1499518

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

GATK/CNVnator alignment

N/A