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 I0 R1	75	34.0	794130	95.7%	759982	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	195,286	T→A	100%	intergenic (‑97/‑82)	USA300HOU_RS00900 ← / → USA300HOU_RS00905	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	195,286	0	T	A	100.0%	116.0 / NA	34	intergenic (‑97/‑82)	USA300HOU_RS00900/USA300HOU_RS00905	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (0/0); new base A (19/15); total (19/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGTTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAAGA  >  USA300TCH1516_ALE/195150‑195420

tGTTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAaaaa                                                                                                                                    <  1:311603/141‑1 (MQ=255)

      tAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATAATCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAatat                                                                                                                              >  2:384234/1‑141 (MQ=255)

           aaaCTTGCTACGACAGAATCTTTATCCATAATGATAGCCCCCTTTATATATGTTTATTTACTTATACCCTACCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTTTCTAAATATTAAAAAAAAAATCTTaa                                                                                                                         >  2:227440/1‑141 (MQ=255)

                              cTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATAATTTTTAGACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATaa                                                                                                      >  1:180402/1‑141 (MQ=255)

                                   tCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAAtt                                                                                                 >  1:307966/1‑141 (MQ=255)

                                         aTGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATGTCCTTGTAATCCGATAAGAATTATAGTa                                                                                           >  1:274853/1‑141 (MQ=255)

                                             tAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAatat                                                                                       >  2:263914/1‑141 (MQ=255)

                                              aGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATACGAATTATAGTAATAtt                                                                                      <  1:195817/141‑1 (MQ=255)

                                                cccccTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTTTAATCCGATAAGAATTATAGTAATAtttt                                                                                    >  2:39627/1‑141 (MQ=255)

                                                    ttatatattTGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCa                                                                                <  1:140058/140‑1 (MQ=255)

                                                    cTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTACTCCGATAAGAATTATAGTAATAttttttaa                                                                                >  1:160646/1‑139 (MQ=255)

                                                     tatatataTGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCaa                                                                               <  1:366948/141‑1 (MQ=255)

                                                     tatatataTGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTCACAGAATTTTATCTAAATAATAAAAAAAATATCTTAATACCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCaa                                                                               <  1:332932/141‑1 (MQ=255)

                                                      ttatatatGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCAAAAAAAAAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAAc                                                                              <  2:362832/140‑1 (MQ=255)

                                                               tttatttaCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTtat                                                                     <  2:101282/141‑1 (MQ=255)

                                                                     taCTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAATTATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATTTTTTTTCAACCATTGTTATaggagg                                                               >  1:344315/1‑141 (MQ=255)

                                                                       cTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGCGGTc                                                             >  2:46704/1‑141 (MQ=255)

                                                                                 aaaaTGATTTTTATACTTTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGa                                                   <  2:315521/138‑1 (MQ=255)

                                                                                 aaCATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGa                                                   <  1:161342/141‑1 (MQ=255)

                                                                                 aaCATGATTTTTATAAATTTTAAAAATATATTTTAAAGTTTTTTCTCTAGGTATCACCATCGAGATCTTAATATCCTTGTAATACGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGa                                                   <  2:379964/141‑1 (MQ=255)

                                                                                         ttttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTAttt                                           <  2:117033/141‑1 (MQ=255)

                                                                                           ttATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTAttttt                                         <  1:128715/141‑1 (MQ=255)

                                                                                               aCTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTttatta                                     >  1:371573/1‑141 (MQ=255)

                                                                                                         aaTATATTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACa                           >  2:66986/1‑141 (MQ=255)

                                                                                                            atatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAAtt                        >  1:349437/1‑140 (MQ=255)

                                                                                                            atatTTTACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATc                        >  1:346709/1‑141 (MQ=255)

                                                                                                               ttttACAGAATTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCttt                     >  2:227174/1‑140 (MQ=255)

                                                                                                                       aaTTTTATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCa             <  1:263914/141‑1 (MQ=255)

                                                                                                                           ttATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCaa         <  1:66986/141‑1 (MQ=255)

                                                                                                                            tATCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGCAATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCaaa        >  2:26641/1‑140 (MQ=255)

                                                                                                                            tATCAAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTCTAGTAATATTTTTTCAACCATTGGTATAGGAGGTCTTACTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAAc        <  1:131934/141‑1 (MQ=255)

                                                                                                                             aTCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAAca       >  2:177784/1‑140 (MQ=255)

                                                                                                                              tCTAAATATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGa      >  2:154783/1‑141 (MQ=255)

                                                                                                                                  aaTATTAAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTAGAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTCTTAGAAGCTAACAATCTTGATTTTGCATCAACGCaaga  >  1:97500/1‑141 (MQ=255)

TGTTTCTAGCTAAACTTGCTACGACAGATTCTTTATCCATAATGATAGCCCCCTATATATATGTTTATTTACTTATACCCTAACATGATTTTTATACTCTTTGAAAATATATTTTACAGAATTTTATCTAAATATTTAAAAAAATATCTTAATATCCTTGTAATCCGATAAGAATTATAGTAATATTTTTTCAACCATTGTTATAGGAGGTCTTATTAATGACATTATTTTTATTAGAAGCTAACAATCTTGATTTTGCATCAACGAAAGA  >  USA300TCH1516_ALE/195150‑195420

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