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
A5 F178 I0 R1	41	49.4	1100758	95.6%	1052324	140.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	USA300TCH1516_ALE	2,454,626	A→T	100%	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	96.4%	164.0 / ‑3.2	54	L48L (CTA→CTT)	lyrA	Lysostaphin resistance protein A
Reads supporting (aligned to +/- strand): ref base A (0/2); new base T (30/22); total (30/24)
Fisher's exact test for biased strand distribution p-value = 1.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTAT  >  USA300TCH1516_ALE/2454494‑2454760

tAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAt                                                                                                                                 <  2:103351/140‑1 (MQ=255)

 aaaaTTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTTTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCAtt                                                                                                                                <  1:110255/140‑1 (MQ=255)

    aTTTCTGGTTTTCAATGGGCAATGACGATTTTTGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAAt                                                                                                                             <  1:258538/140‑1 (MQ=255)

         tGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCCGTGTATAATTAGGGTCAAACCCTTTATATCTGAACTTCCAGATCTTGCACCATTACTtcctg                                                                                                                        >  2:430109/1‑140 (MQ=255)

         tGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTAAATAATTGGTGTCAAAAACTTTATATTTGAAGTTACAGATCTTGCACCATTAATtgctg                                                                                                                        >  2:35373/1‑140 (MQ=255)

           gTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCa                                                                                                                      <  1:221684/140‑1 (MQ=255)

                        aaTGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATAc                                                                                                         <  2:183137/140‑1 (MQ=255)

                          tGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTc                                                                                                       <  2:455675/140‑1 (MQ=255)

                             cGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCAATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGtt                                                                                                    >  2:265511/1‑140 (MQ=255)

                                ttttCGTCTTCTTTGTCATCACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCAATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTc                                                                                                 >  1:330960/1‑140 (MQ=255)

                                ttttCGTCTTCTTTCTCGTTACAATGGCGCTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTc                                                                                                 >  1:294417/1‑140 (MQ=255)

                                gtttCGTCTTCTTTTTTATTAACATGGAGTTATCCATTATGCTCAGTTATTTCCTGTCTATAATTTGTGTCAAACACTTTATATTTGAAGTTACATATCTTGCACCATTAATTAATTAAAGCATTTTTATACTCGTTTTc                                                                                                 <  2:530170/139‑1 (MQ=255)

                                     gttttcttTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAata                                                                                            <  2:52011/137‑1 (MQ=255)

                                            ttGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAg                                                                                     >  1:413087/1‑140 (MQ=255)

                                                  ttACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGGACCATTACTTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCaa                                                                               >  1:405886/1‑140 (MQ=255)

                                                  taaCAATGGCGTTATCCAGTATGCTAACAAGTAGCCAGTCTATAAATGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTCCGGCAATCATTTGTATACTAGTTTTCAATTATAAAAAgggcaaa                                                                               >  2:503655/3‑135 (MQ=255)

                                                           cGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGt                                                                      <  1:23511/140‑1 (MQ=255)

                                                             ttATCCCTTATTCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGttt                                                                    <  2:282625/140‑1 (MQ=255)

                                                             ttATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGttt                                                                    >  1:229964/1‑140 (MQ=255)

                                                             gtATCCATTATGCTCAGAGTTTTCCATTTTATAATTGGTGTCAAACAATACAAATGTGAAGTTACATATCTTTCACGATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGttt                                                                    <  2:73349/139‑1 (MQ=255)

                                                                tCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTaaa                                                                 >  1:413250/1‑140 (MQ=255)

                                                                  cATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTCAAAt                                                               >  2:365829/1‑140 (MQ=255)

                                                                    ttATGCTGACAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATtc                                                             <  2:92011/140‑1 (MQ=255)

                                                                    ttATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAAtac                                                             >  1:133157/1‑138 (MQ=255)

                                                                       tGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCa                                                          <  1:321564/140‑1 (MQ=255)

                                                                         cTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATCTTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAACATTCTCAAt                                                        >  2:132439/1‑140 (MQ=255)

                                                                          tCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATc                                                       <  2:244602/140‑1 (MQ=255)

                                                                          tCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATc                                                       <  1:268502/140‑1 (MQ=255)

                                                                            agagATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAg                                                     >  2:494304/1‑140 (MQ=255)

                                                                               gaTTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCt                                                  >  2:174654/1‑140 (MQ=255)

                                                                                 ttgccAGGCTAGAATTGGTGTCAAACGCTTTATATTTGAAGTTACAGTTCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGGCCAGCGTGCAGGTTTAAGATTCTCAAGCAGGCTGa                                                <  2:109099/137‑1 (MQ=255)

                                                                                     cAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGt                                            >  2:371338/1‑140 (MQ=255)

                                                                                     cAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGt                                            >  1:215682/1‑140 (MQ=255)

                                                                                     cAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAAATGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGt                                            >  1:171089/1‑140 (MQ=255)

                                                                                      aGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCACGTTTAAAATTCTCCATCAGCCCGAAAGTa                                           >  2:234862/1‑140 (MQ=255)

                                                                                          tataATTGGTGTCATACACTTTATACTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGCCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTg                                       <  1:334395/140‑1 (MQ=255)

                                                                                               ttGGTGGCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGt                                  >  2:304886/1‑140 (MQ=255)

                                                                                                   tgtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTAt                              <  1:190432/140‑1 (MQ=255)

                                                                                                    gtCAAACACTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTAtt                             >  1:208268/1‑140 (MQ=255)

                                                                                                         acacTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCGTGAAAGTAATTGAACGTCTATTGCTAg                        >  2:492136/1‑140 (MQ=255)

                                                                                                         acacTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAg                        >  2:547497/1‑140 (MQ=255)

                                                                                                          cacTTTATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGc                       >  2:151175/1‑140 (MQ=255)

                                                                                                           acTTTATATTTGAAGTTACTGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCt                      <  2:336143/140‑1 (MQ=255)

                                                                                                           acTTTATATTTGAAGTTACAGATCTTTCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCt                      <  2:508783/140‑1 (MQ=255)

                                                                                                             tttATATTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAGTAATTTGTATACGCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCttt                    <  1:260196/140‑1 (MQ=255)

                                                                                                               tataTTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTCTATTAGTTAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTaa                  <  1:400541/140‑1 (MQ=255)

                                                                                                                atatTTGAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAAt                 >  1:235664/1‑140 (MQ=255)

                                                                                                                      gAAGTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTATATTGCTAACTTTAATTTTAcc           >  2:147749/1‑140 (MQ=255)

                                                                                                                         gTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATAGTCGTTTTCGATTATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTAAACGTCTATTGCTAGCTTTAATTTTACCttt        >  1:211322/1‑140 (MQ=255)

                                                                                                                         gTTACAGATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAAGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCttt        >  1:443420/1‑140 (MQ=255)

                                                                                                                          ttACAGATTTTGCACTATTAATTGCTGCAATCATTTTTATACTCGTTTTTAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTa       <  1:78526/140‑1 (MQ=255)

                                                                                                                              aGATCTTGCACCATTAATAGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAatta   >  2:233096/1‑140 (MQ=255)

                                                                                                                               gATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAattat  <  2:511316/140‑1 (MQ=255)

                                                                                                                               gATCTTGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCAAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTCCCTTTActtct  >  2:134958/1‑138 (MQ=255)

TAAAATTTCTGGTTTTCAATGGGCAATGACGATTTTCGTCTTCTTTGTCATTACAATGGCGTTATCCATTATGCTCAGAGATTTCCAGTCTATAATTGGTGTCAAACACTTTATATTTGAAGTTACAGATCTAGCACCATTAATTGCTGCAATCATTTGTATACTCGTTTTCAAATATAAAAAGGTCCAACTTGCAGGTTTAAAATTCTCAATCAGCCTGAAAGTAATTGAACGTCTATTGCTAGCTTTAATTTTACCTTTAATTAT  >  USA300TCH1516_ALE/2454494‑2454760

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