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 F58 I0 R1 46 56.2 1222162 96.0% 1173275 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,455,698 C→A 100% H406N (CAT→AAT) ‡ lyrA → Lysostaphin resistance protein A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,455,6980CA76.3% 67.0 / 23.2 46H406N (CAT→AAT) ‡lyrALysostaphin resistance protein A
Reads supporting (aligned to +/- strand):  ref base C (5/5);  new base A (18/14);  total (25/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01
Rejected as polymorphism: Polymorphic base substitution creates a homopolymer stretch.

TAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACC  >  USA300TCH1516_ALE/2455571‑2455831
                                                                                                                               |                                                                                                                                     
tAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACt                                                                                                                         >  1:68235/1‑141 (MQ=255)
tAAACAAGCACCACAAAGTGAAGATTTAACAAACGATTCAAATGACGATGGAATAGAGCAATCATTAAAAGAACCTGCGAGTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATTCA‑AAAAAATTATCGAAGAAGCt                                                                                                                         >  1:583146/1‑141 (MQ=255)
  aaCAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACAGATCGAAAAAACTg                                                                                                                        >  2:402410/1‑141 (MQ=255)
      aGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTgaagaa                                                                                                                   <  1:28334/141‑1 (MQ=255)
         accacAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACa                                                                                                                 <  2:27467/141‑1 (MQ=255)
           cacaAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATc                                                                                                              >  1:542971/1‑141 (MQ=255)
             caAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCtt                                                                                                            >  1:529689/1‑141 (MQ=255)
             caAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCtt                                                                                                            >  2:467703/1‑141 (MQ=255)
                  tGACGATTGAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGAt                                                                                                       <  1:110813/141‑1 (MQ=255)
                         ttAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAAc                                                                                                 <  1:374998/141‑1 (MQ=255)
                               accGATTCAAATGAAGACAAAATAGAGGAATCATTAAACGATCCTGCGACTTATAAAGAAGACAGATGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAaataa                                                                                           <  2:455860/139‑1 (MQ=255)
                                 agATTCAAATGAAGATGAAACAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAATA‑ATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAAtaataa                                                                                        <  2:537021/140‑1 (MQ=255)
                                  gATTCAAATGAAGATGAAACAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAAc                                                                                       <  1:18539/141‑1 (MQ=255)
                                    ttCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACa                                                                                      >  1:145292/1‑141 (MQ=255)
                                     tCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGGAGACAAACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACaaa                                                                                    <  2:218742/141‑1 (MQ=255)
                                        aaTGAAGATGAAATAGCGCAATCATTAAAAGAAGCTGCGACTTATAAAGAAGATAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgc                                                                                  <  2:500573/141‑1 (MQ=255)
                                        aaTGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgc                                                                                  >  2:427304/1‑141 (MQ=255)
                                        aaTAAAGAAGAAAAAGAGCAATCATTAAAAGAACCTGCAACTTATAAAGAAGACAGACGTTCATCAGTTGAAATAAAAAAA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAgcg                                                                                 <  2:542832/141‑1 (MQ=255)
                                          tGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCt                                                                               <  1:166431/141‑1 (MQ=255)
                                              gATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCt                                                                           <  1:587174/141‑1 (MQ=255)
                                                 gAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGGCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGt                                                                        <  1:322128/141‑1 (MQ=255)
                                                       gagCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACctct                                                                  >  1:421427/1‑141 (MQ=255)
                                                           aaTCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTGGCTAGTACCTCTTaa                                                               >  1:443433/1‑141 (MQ=255)
                                                             tCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaa                                                             <  1:520430/141‑1 (MQ=255)
                                                             tCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTaaaaa                                                            >  1:128690/1‑141 (MQ=255)
                                                                ttAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAAAAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgaa                                                         >  2:215703/1‑140 (MQ=255)
                                                                   aaaGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAgatga                                                       >  1:251373/1‑141 (MQ=255)
                                                                     aGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGc                                                    >  1:176662/1‑141 (MQ=255)
                                                                        aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAGAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAGATGATGCTaa                                                 >  2:411365/1‑140 (MQ=255)
                                                                        aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAg                                                 <  2:68235/141‑1 (MQ=255)
                                                                        aCCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAg                                                 >  1:284641/1‑141 (MQ=255)
                                                                         ccTGCGACTTATAACGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGc                                                >  2:413992/1‑141 (MQ=255)
                                                                         ccTGCGACTTATAAAGAAGACAGACGTACATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAGCAAATAATAACAAAGGGCTCGCTAGTACCTCTTAAAAAAATGATGCTaaa                                                >  2:416720/1‑139 (MQ=255)
                                                                          ctacGACTCAAAAAGAAGAAAGACGTTCATCAGTTGAAAAAAAAAAA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCa                                               <  2:230934/138‑1 (MQ=255)
                                                                             cGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACGCCTTAAAAAAATGATGCTAGCAAgg                                            >  1:107247/1‑140 (MQ=255)
                                                                               aCTTATAAAGAAGACCGACGTTCATCAGTTGTAATTGATGCAATAAAA‑TTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATATCAAAGCGCTTGCTAGTACCTCTTAAAAAGATGAGGCTAGCATgcgc                                          <  1:430522/141‑1 (MQ=255)
                                                                               aCTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgc                                          <  2:251828/141‑1 (MQ=255)
                                                                                  tataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAgcgtaat                                       <  2:6040/141‑5 (MQ=255)
                                                                                  tataAAGAAGACAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCttt                                       <  1:144505/141‑1 (MQ=255)
                                                                                        gaagaCAGACGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTctata                                 >  1:107657/1‑141 (MQ=255)
                                                                                           gacagacGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGGTAGCAACCGATTTTctatacta                              >  2:393948/1‑141 (MQ=255)
                                                                                                acGTTCATCAGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTatatat                         >  1:213092/1‑141 (MQ=255)
                                                                                                        caGTTGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTc                 <  2:24142/141‑1 (MQ=255)
                                                                                                            tGTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTAAATATTATTTTTCTaaa             >  1:4996/1‑141 (MQ=255)
                                                                                                             gTAATTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTAGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTaaaa            >  2:188147/1‑141 (MQ=255)
                                                                                                               aaTTGATGCA‑AAAAAATTATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAAtt          >  1:376172/1‑141 (MQ=255)
                                                                                                                        gaaaaaaaGTATCGAAAAAACTGAAGATCAATTTTCAGATAAAAATAAATAATAACAATGCGCTTGCTAGTACCTCTTAAAAAGATTATGCTAGCCAGCGCTTTTCTATACTCTATATTATTTTTCTAAAATTTTAACAcc  <  2:258512/139‑1 (MQ=255)
                                                                                                                               |                                                                                                                                     
TAAACAAGCACCACAAAGTGACGATTTAACAAACGATTCAAATGAAGATGAAATAGAGCAATCATTAAAAGAACCTGCGACTTATAAAGAAGACAGACGTTCATCAGTTGTAATTGATGCAGAAAAACATATCGAAAAAACTGAAGAACAATCTTCAGATAAAAACAAATAATAACAAAGCGCTTGCTAGTACCTCTTAAAAAGATGATGCTAGCAAGCGCTTTTCTATACTATATATTATTTTTCTAAAATTTTAACACC  >  USA300TCH1516_ALE/2455571‑2455831

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A