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 F52 I0 R1	39	94.7	2129336	96.2%	2048421	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,454,626	A→T	74.9%	L48L (CTA→CTT)	lyrA →	Lysostaphin resistance protein A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,454,626	0	A	T	74.9%	203.2 / 65.0	111	L48L (CTA→CTT)	lyrA	Lysostaphin resistance protein A
Reads supporting (aligned to +/- strand): ref base A (16/12); new base T (34/47); total (51/60)
Fisher's exact test for biased strand distribution p-value = 1.91e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 111 total aligned reads displayed.

AACAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTATTC  >  USA300TCH1516_ALE/2454489‑2454762

aaCAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACACTGGCGTTATCCATTATGCTCAGAGATTTACAGTCTATAATTGGTGCCAAACACTTTATATTTTCAGTTAACGATTTAggc                                                                                                                                        >  2:257875/1‑139 (MQ=255)

aaCAATAAAATTTCTGGTTTTCAATGGGCAATGACGAGTTTCGTCTTCTTTGTTATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCa                                                                                                                                        >  1:823119/1‑141 (MQ=255)

  cAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCAcc                                                                                                                                      >  1:942390/1‑141 (MQ=255)

  cAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCAcc                                                                                                                                      <  2:563500/141‑1 (MQ=255)

   aaTAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTTCAGATCTTGCACCa                                                                                                                                     >  2:556594/1‑141 (MQ=255)

   aaTAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCa                                                                                                                                     >  2:292025/1‑141 (MQ=255)

     tAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAtt                                                                                                                                   <  1:482615/141‑1 (MQ=255)

     tAAAATTTCTGGTTTCTAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAtt                                                                                                                                   <  1:112389/141‑1 (MQ=255)

      aaaaTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTa                                                                                                                                  >  2:949202/1‑141 (MQ=255)

      aaaaTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTa                                                                                                                                  >  2:280990/1‑141 (MQ=255)

        aaTTTCTGGTTTTCAATGGGCAATGACGCTTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCCTTCAt                                                                                                                                >  2:23889/1‑141 (MQ=255)

        aaTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGCTCTTGCACTATTAAt                                                                                                                                >  2:331916/1‑141 (MQ=255)

        aaTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAAt                                                                                                                                <  2:101892/141‑1 (MQ=255)

        aaTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTact                                                                                                                                >  2:23820/1‑139 (MQ=255)

        aaTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGCTACCGATCTTTCACCATTGAt                                                                                                                                >  2:257475/1‑141 (MQ=255)

         agttCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAAtt                                                                                                                               <  1:237028/139‑1 (MQ=255)

         aTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAAtt                                                                                                                               >  2:455240/1‑141 (MQ=255)

           ttCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATtgc                                                                                                                             <  1:917527/141‑1 (MQ=255)

           ttCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTATTTGGCAGTACAATGGCGTTATCCATAATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATtgc                                                                                                                             <  1:717865/141‑1 (MQ=255)

                gTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGGAAATACACACCGTGCACCATTAATTGCTGCaa                                                                                                                        <  1:254523/141‑1 (MQ=255)

                     cAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCAtt                                                                                                                   <  1:252581/141‑1 (MQ=255)

                     cAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCAtt                                                                                                                   <  1:659111/141‑1 (MQ=255)

                      aaTGGGCAATGACGATTTTCGTCTTCTTTGTCATTCCAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCAttt                                                                                                                  >  2:834491/1‑141 (MQ=255)

                       aTGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCAGTATGCCCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCCCCATTAATTGCTGCCATCATTTg                                                                                                                 >  2:510875/1‑141 (MQ=255)

                             aaTGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCATACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACt                                                                                                           <  1:668604/141‑1 (MQ=255)

                              aTGACCACTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTc                                                                                                          <  1:1056829/141‑1 (MQ=255)

                               tGACGATTATCGTCTTCTTTGTCATTACAATCAAGTTTTCCATTCTCCTCTTTCAGGGGCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCg                                                                                                         >  2:748632/1‑141 (MQ=255)

                                gACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGt                                                                                                        >  1:37910/1‑141 (MQ=255)

                                    aTTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCCTTAATTGCTGCAATCATTTGTATACTCGt‑ttta                                                                                                   >  1:333905/1‑140 (MQ=255)

                                         cGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAata                                                                                              >  2:862982/1‑141 (MQ=255)

                                           tcttctTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAAtata                                                                                            <  1:331865/141‑1 (MQ=255)

                                                 ttGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAgg                                                                                      >  2:124999/1‑141 (MQ=255)

                                                   gTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTc                                                                                    <  1:69124/141‑1 (MQ=255)

                                                   gTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCGATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTc                                                                                    >  1:602332/1‑141 (MQ=255)

                                                    tCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTcc                                                                                   >  2:592432/1‑141 (MQ=255)

                                                      aTTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTAGAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCaa                                                                                 <  1:573087/141‑1 (MQ=255)

                                                       ttACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAAc                                                                                <  2:626415/141‑1 (MQ=255)

                                                        tACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCCAATATAAAAAGGTCCAACt                                                                               >  1:189205/1‑141 (MQ=255)

                                                         aCAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACtt                                                                              >  1:727328/1‑141 (MQ=255)

                                                         aCAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACtt                                                                              >  1:321528/1‑141 (MQ=255)

                                                           aaTGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGc                                                                            <  1:980928/141‑1 (MQ=255)

                                                           aaTGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGc                                                                            <  2:52595/141‑1 (MQ=255)

                                                             tGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAg                                                                          <  1:510459/141‑1 (MQ=255)

                                                              ggCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAgg                                                                         <  1:945549/141‑1 (MQ=255)

                                                                cGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTTCAACTGGCacatc                                                                       <  2:757699/141‑5 (MQ=255)

                                                                cGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGtt                                                                       <  1:802752/141‑1 (MQ=255)

                                                                   tATCCATTATGCTCAGAGACTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACTATTAATTGTTGCACTCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTaa                                                                    >  2:832856/1‑141 (MQ=255)

                                                                    aTCCAATATGGTCCTAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTaaa                                                                   <  2:454054/141‑1 (MQ=255)

                                                                       cATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAAtt                                                                >  2:844750/1‑141 (MQ=255)

                                                                        aTTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATtc                                                               <  2:507270/141‑1 (MQ=255)

                                                                        aTTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCTGGTTTAAAATtc                                                               <  1:180688/141‑1 (MQ=255)

                                                                             gCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAAt                                                          >  1:782294/1‑141 (MQ=255)

                                                                             gCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAAt                                                          >  1:898977/1‑141 (MQ=255)

                                                                              cccAGAGAGTTCCAGTCTACAATTGGTGTCAAACACTTTATATGTGACGTTACAGATCTAGCACCATTCCTTTATGCATTTCCTTGGA‑AGCCGTGTTTCAAATATAAAAAGGCCCAACTTGCAGGTTTAAAATTCTCAATc                                                         <  1:508778/139‑1 (MQ=255)

                                                                              cTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATc                                                         <  1:862982/141‑1 (MQ=255)

                                                                              cTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATc                                                         <  1:368378/141‑1 (MQ=255)

                                                                              cTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATc                                                         <  1:978539/141‑1 (MQ=255)

                                                                               tCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCa                                                        >  2:234477/1‑141 (MQ=255)

                                                                               tCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCa                                                        <  1:455240/141‑1 (MQ=255)

                                                                               tCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCa                                                        >  2:798685/1‑141 (MQ=255)

                                                                                cAGAGATTTTCAGCCGATAATTTGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAg                                                       <  1:414782/141‑1 (MQ=255)

                                                                                cAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACTGATCTGGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAg                                                       <  1:854398/141‑1 (MQ=255)

                                                                                cAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAg                                                       >  1:66417/1‑141 (MQ=255)

                                                                                 agagATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGc                                                      <  1:954390/141‑1 (MQ=255)

                                                                                 agagATGTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAATTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTACAACTTGCAGGTTTAAAATTCTCAATCAGc                                                      <  2:518507/141‑1 (MQ=255)

                                                                                  gagaTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGcc                                                     >  2:969536/1‑141 (MQ=255)

                                                                                       ttCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGaaa                                                >  2:735214/1‑141 (MQ=255)

                                                                                       ttCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAATTTGCAGGTTTAAAATTCTCATTCAGCCTGaaa                                                >  2:505553/1‑141 (MQ=255)

                                                                                        tCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAg                                               <  1:711407/141‑1 (MQ=255)

                                                                                        tCCAGTCTATAATTGGTGTCAAACACTTTATATGTGAAGTTACAGATCTTGCACCATTAAGTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAg                                               >  2:619314/1‑141 (MQ=255)

                                                                                          cAGTCTATAATTGGTTTCAAACCCTTTATATTTTAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTa                                             <  2:690624/141‑1 (MQ=255)

                                                                                           aGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTaa                                            <  1:280990/141‑1 (MQ=255)

                                                                                           aGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTaa                                            <  1:949202/141‑1 (MQ=255)

                                                                                           aGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTaa                                            <  1:802490/141‑1 (MQ=255)

                                                                                           aGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTaa                                            <  2:617423/141‑1 (MQ=255)

                                                                                             tCTATAATTGGTGTAAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAAtt                                          <  1:397626/141‑1 (MQ=255)

                                                                                              ttataATTTGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTg                                         <  1:18412/140‑1 (MQ=255)

                                                                                              cTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTg                                         <  1:342687/141‑1 (MQ=255)

                                                                                               tataATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGa                                        <  2:57825/141‑1 (MQ=255)

                                                                                                  aaTTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCACTCAGCCTGAAAGTAATTGAACg                                     >  1:738705/1‑141 (MQ=255)

                                                                                                       gtgtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTAt                                <  1:325312/141‑1 (MQ=255)

                                                                                                       gagtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCTAATATAAAAAGGTCCAACTTGCAGGATTAAAATTTTCAATCAGCCTGAAAGTAATTTAAGCTCTAt                                <  1:779439/139‑1 (MQ=255)

                                                                                                          tCAAACACTTTATATTTGAAGTTACAGATCCAGGACGATGAATTGCTGCAATTAGTTGTTTACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGc                             >  2:748666/1‑141 (MQ=255)

                                                                                                           cAAACTCTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCt                            <  2:388915/141‑1 (MQ=255)

                                                                                                           cAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCt                            <  1:592432/141‑1 (MQ=255)

                                                                                                                   ttATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTATaa                    >  2:52221/1‑141 (MQ=255)

                                                                                                                   ttATATTTGAAGTTACAGATCTTGCACCATAAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTaa                    <  1:628837/141‑1 (MQ=255)

                                                                                                                        tttGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTa               <  2:602332/141‑1 (MQ=255)

                                                                                                                           gAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAGATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGTTCGGTTGAATTTTACCt            >  1:144479/1‑141 (MQ=255)

                                                                                                                            aaGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCtt           <  2:262571/141‑1 (MQ=255)

                                                                                                                              ggtACCGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTa         <  2:841785/139‑1 (MQ=255)

                                                                                                                              gTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTa         <  2:545045/141‑1 (MQ=255)

                                                                                                                              gTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTa         >  2:327733/1‑141 (MQ=255)

                                                                                                                               ttACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTaa        <  1:136187/141‑1 (MQ=255)

                                                                                                                                 aCAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAatt      >  1:841631/1‑141 (MQ=255)

                                                                                                                                 aCAGATCTTGCACCATTAATTGCTGCAATCATTTGTATAATCGT‑TGTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAatt      >  1:466454/1‑141 (MQ=255)

                                                                                                                                  cAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATAT‑AAAAGGGCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTCATTTTACCTTTAaatat    >  2:710926/1‑141 (MQ=255)

                                                                                                                                   aGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAattat    >  2:412022/1‑141 (MQ=255)

                                                                                                                                    gATCTTGCACCATGAATTGCTGCAAGCATTTGGATACTAGT‑TTTCAAATATAAAAAGGACCAACTTACAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGTACGTCTACTGCTAGCTTTAATTGTACCTTTAattatt   <  2:792104/141‑1 (MQ=255)

                                                                                                                                    gATCTAGCAGCATTAATTGCTACAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAattatt   >  1:779236/1‑141 (MQ=255)

AACAATAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGT‑TTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTATTC  >  USA300TCH1516_ALE/2454489‑2454762

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