Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 322,258 A→G 9.1% A7A (GCA→GCG)  lytM_2 → Glycyl‑glycine endopeptidase LytM

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE322,2580AG 9.1% 103.2 / 2.2 41A7A (GCA→GCG) lytM_2Glycyl‑glycine endopeptidase LytM
Reads supporting (aligned to +/- strand):  ref base A (15/22);  new base G (2/2);  total (17/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.69e-01

AATATTAAATAGTTGGAAAATGAGAATTAAATCCTTTACTCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGACGTATCTTATGGTACTTATTATACAATT  >  USA300TCH1516_ALE/322119‑322396
                                                                                                                                           |                                                                                                                                          
aaTATTAAATAGTTGGAAAATGAGAATTAAATCCTTTACTCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAAcagcagcag                                                                                                                                           >  1:22854/1‑141 (MQ=255)
aaTATTAAATAGTTGGAAAATGAGAATTAAATCCTTTACTCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAAcagcagcag                                                                                                                                           >  1:299435/1‑141 (MQ=255)
      aaaTAGTTGGAAAATGAGAATTAAATCCTTTACTCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTg                                                                                                                                     >  2:318787/1‑141 (MQ=255)
         tAGTTGGAAAATGAGAATTAAATCCTTTACTCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCaa                                                                                                                                  <  2:234521/141‑1 (MQ=255)
             tGGAAAATGAGAATTAAATCCTGTACTCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTAAACATGAAAAAATTAACAGCAGCAGCGATTGCAACGAt                                                                                                                              <  2:306874/141‑1 (MQ=255)
                aaaaTGAGAATTAAATCCTTTACTCATTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATggg                                                                                                                           <  2:76993/141‑1 (MQ=255)
                            aaaTCCTTTACTCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCGGCGATTGCAACGATGGGCTTCGCTACAtt                                                                                                               >  1:280058/1‑141 (MQ=255)
                            aaaTCCTTTACTCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCGGCGATTGCAACGATGGGCTTCGCTACAtt                                                                                                               >  1:326577/1‑141 (MQ=255)
                             aaTCCTTTACTCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACAttt                                                                                                              >  2:335743/1‑141 (MQ=255)
                               tCCTTTACTCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACCATTAc                                                                                                            >  2:65484/1‑141 (MQ=255)
                                 cTTTACTCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACaa                                                                                                          <  2:334616/141‑1 (MQ=255)
                                       tCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGgcgc                                                                                                    <  1:119030/141‑1 (MQ=255)
                                               cTAATTCTTTGAGTCTGTGCAGTACAGTTAAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAACa                                                                                            >  2:55038/1‑141 (MQ=255)
                                                    ttttttAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATgc                                                                                       <  2:107309/139‑1 (MQ=255)
                                                      ttttAGTATGTGCAGTAAAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATgcag                                                                                     <  2:177092/141‑1 (MQ=255)
                                                       tttAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATgcagc                                                                                    >  1:37374/1‑141 (MQ=255)
                                                        ttAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATgcagca                                                                                   <  1:359813/141‑1 (MQ=255)
                                                         tAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATgcagcaa                                                                                  >  1:126830/1‑140 (MQ=255)
                                                          attATGTGCAGTGCAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTAAACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGa                                                                                 <  2:96255/139‑1 (MQ=255)
                                                          aGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGa                                                                                 >  2:342398/1‑141 (MQ=255)
                                                                 gCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACa                                                                          <  2:302494/141‑1 (MQ=255)
                                                                       cAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACAcc                                                                    >  2:75251/1‑141 (MQ=255)
                                                                           ttAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCcaac                                                                <  2:337320/141‑1 (MQ=255)
                                                                                  aaaaCTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGcaca                                                         <  1:211806/141‑1 (MQ=255)
                                                                                     actaactTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATac                                                      <  1:90503/141‑1 (MQ=255)
                                                                                             taactttaaTGGAGGATCTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGt                                              <  2:183326/141‑1 (MQ=255)
                                                                                                    aaTGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCGGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAAcaca                                       <  2:326577/141‑1 (MQ=255)
                                                                                                    aaTGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCGGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAAcaca                                       <  2:280058/141‑1 (MQ=255)
                                                                                                          ggaTGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATcaca                                 <  2:328658/141‑1 (MQ=255)
                                                                                                          ggaTGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATcaca                                 <  2:328685/141‑1 (MQ=255)
                                                                                                            aTGTTGTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAg                               <  2:105087/141‑1 (MQ=255)
                                                                                                             tggtttATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGa                              <  2:71895/138‑1 (MQ=255)
                                                                                                             tGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGa                              <  2:186901/141‑1 (MQ=255)
                                                                                                               ttttATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGACg                            <  1:157434/141‑1 (MQ=255)
                                                                                                                tttATACATGAAAAAATTAACAGCATCAGCGATTCCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGACGt                           <  1:198520/141‑1 (MQ=255)
                                                                                                                    taCATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGACGTATCt                       >  1:44487/1‑141 (MQ=255)
                                                                                                                      cATGAAAAAATTAACAGCAGCACCGATTGCAACGATGGGCTTCGCTACATTTACAATAGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGCCAACACAATCACAAGACGTATCTTa                     >  2:214992/1‑141 (MQ=255)
                                                                                                                       aTGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGACGTATCTTAt                    <  1:374610/141‑1 (MQ=255)
                                                                                                                          aaaaaaTTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGACGTATCTTATGGt                 >  2:226131/1‑141 (MQ=255)
                                                                                                                               aTTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGACGTATCTTATGGTACtta            >  1:80575/1‑141 (MQ=255)
                                                                                                                               aTTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGACGTATCTTATGGTACtta            >  1:78348/1‑141 (MQ=255)
                                                                                                                                  aaCAGCAGCAGCGATTGCAACGATGGGCTTCGCTCCATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGACGTATCTTATGGTACttatta         >  1:332582/1‑141 (MQ=255)
                                                                                                                                   aCAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGACGTATCTTATGGTACAtattat        >  1:174610/1‑141 (MQ=255)
                                                                                                                                         gcagcGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACAACAAACACCCAACAAGCACATACACAAAGGTCAACACAATCACAAGACGTATCTAATGGTACTTATTATACAAtt  >  2:23315/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                          
AATATTAAATAGTTGGAAAATGAGAATTAAATCCTTTACTCAGTTGTCTAATTCTTTTAGTATGTGCAGTACAGTTTAATTGAAAACTAACTTTAACTTTAATGGAGGATGTTTTATACATGAAAAAATTAACAGCAGCAGCGATTGCAACGATGGGCTTCGCTACATTTACAATGGCGCATCAAGCAGATGCAGCAGAAACGACAAACACCCAACAAGCACATACACAAATGTCAACACAATCACAAGACGTATCTTATGGTACTTATTATACAATT  >  USA300TCH1516_ALE/322119‑322396

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: ‑