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
A9 F174 I0 R1	34	41.4	875437	98.7%	864056	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	1,909,486:1	+T	100%	coding (293/303 nt)	USA300HOU_RS09460 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,909,486	1	.	T	100.0%	97.1 / NA	30	G98V (GGT→GTT)	USA300HOU_RS09460	hypothetical protein
Reads supporting (aligned to +/- strand): ref base . (0/0); new base T (12/18); total (12/18)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TTGTCTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAATCATAACTATGC  >  USA300TCH1516_ALE/1909347‑1909621

ttGTCTATAATTTTTGCAGATCGTTCAATGAAATCACGAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑t                                                                                                                                        <  1:114589/141‑1 (MQ=255)

       taATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑tttttatt                                                                                                                                 >  1:5859/1‑137 (MQ=255)

         aTTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTtttattta                                                                                                                                >  1:144459/1‑141 (MQ=255)

                         cAAGTAAATCACTAAAGCCTGATGCAGATTTGACTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTCTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTc                                                                                                                <  1:411422/141‑1 (MQ=255)

                           aTTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAATAAAGTTAATATGTCAt                                                                                                              >  1:369774/1‑141 (MQ=255)

                                   aCTAAAGCCCGATGCAGATTGGATTAGAATTGAGCTTGCTTTGGTTCTTTGGCTTGATCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGcat                                                                                                      >  1:638026/1‑139 (MQ=255)

                                         gcatGATGCAGATTGGATTAGGATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATAc                                                                                                <  1:408109/138‑1 (MQ=255)

                                                gCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAacaa                                                                                         <  1:94030/141‑1 (MQ=255)

                                                     ttGGATTAGAATTGCGTGTAAAAGTTTGACTTGGATTATTCTAAAACTTGATAAATAACATAGCTTTCCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAacaatacaa                                                                                    <  1:377203/141‑1 (MQ=255)

                                                     ttGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAacaatacaa                                                                                    <  1:656724/141‑1 (MQ=255)

                                                       ggATGAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATg                                                                                  <  1:78923/141‑1 (MQ=255)

                                                                  gCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCCTGCtat                                                                       >  1:358828/1‑141 (MQ=255)

                                                                       tAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGa                                                                  <  1:13416/141‑1 (MQ=255)

                                                                       tAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGa                                                                  <  1:13196/141‑1 (MQ=255)

                                                                         aaaGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGt                                                                <  1:144112/141‑1 (MQ=255)

                                                                          aaGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTa                                                               <  1:322474/141‑1 (MQ=255)

                                                                                  cTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAAtt                                                       <  1:223658/141‑1 (MQ=255)

                                                                                        ttattCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATaa                                                 <  1:84111/141‑1 (MQ=255)

                                                                                        ttattCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGGAAAACAATTTGCTaa                                                 >  1:793163/1‑141 (MQ=255)

                                                                                                    ttATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGta                                     >  1:871196/1‑141 (MQ=255)

                                                                                                       ttttAGTACATATCTTTTCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATaa                                  >  1:480383/1‑141 (MQ=255)

                                                                                                         ttAGTACATATCTTTTAAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATaaaa                                <  1:21700/141‑1 (MQ=255)

                                                                                                            gTACATATCTTTTCTATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAat                             >  1:569103/1‑141 (MQ=255)

                                                                                                              gcacatCTTTCGAAGTGGTCGGACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAatat                           <  1:825443/137‑1 (MQ=255)

                                                                                                                      tttCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGAtttt                   <  1:730442/141‑1 (MQ=255)

                                                                                                                      tttCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGAtttt                   <  1:870050/141‑1 (MQ=255)

                                                                                                                      tttCAATTGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGAtttt                   >  1:272082/1‑141 (MQ=255)

                                                                                                                            ttGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAAt             >  1:659214/1‑141 (MQ=255)

                                                                                                                            ttGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAAt             <  1:295878/141‑1 (MQ=255)

                                                                                                                            ttGTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAAt             >  1:286966/1‑141 (MQ=255)

                                                                                                                              gTTCGTACATTCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGGTAACGTTGTTGCGTATAAAAAATATTCGATTTTCGCAAGCa           >  1:108347/1‑141 (MQ=255)

                                                                                                                                       ttCGGTTTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAATCATAACTATGc  <  1:244845/141‑1 (MQ=255)

TTGTCTATAATTTTTGCAGATCGTTCAATTAAATCACTAAAGCCTGATGCAGATTGGATTAGAATTGCGAGTAAAAGTTTGCCTTGGATTATTCTAATTGTTATTTTAGTACATATCTTTTCAATTGTTCGTACATTCGG‑TTTTATTTAAAAAAGTTAATATGTCATTGTAGCCTTAATACAAAACAATACAATGTATCATGCTATAATGAGTAAAACAATTTGATAACGTTGTTGCGTATAAAAAATATTAGATTTTCGAAATCATAACTATGC  >  USA300TCH1516_ALE/1909347‑1909621

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