Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,474,639 C→G 100% A9129P (GCA→CCA)  ebh_1 ← Extracellular matrix‑binding protein ebh

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,474,6390CG100.0% 127.6 / NA 39A9129P (GCA→CCA) ebh_1Extracellular matrix‑binding protein ebh
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (20/19);  total (20/19)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGCGACCTTTAAATCCATCTTGTTGAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGCTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTACAGTTTGCTCAACGTTAGCA  >  USA300TCH1516_ALE/1474501‑1474766
                                                                                                                                          |                                                                                                                               
tGCGACCTTTAAATCCATCTTGTTGAGCATTGTTTAATGCATTAAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGtt                                                                                                                               >  2:315754/1‑141 (MQ=255)
   gACCTTTAAATCCATCTTGTTGAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGAt                                                                                                                            <  2:185132/141‑1 (MQ=255)
    aCCTTTAAATCCATCTTGTTGAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATc                                                                                                                           >  2:81368/1‑141 (MQ=255)
    aCCTTTAAATCCATCTTGTTGAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATc                                                                                                                           >  2:341004/1‑141 (MQ=255)
       tttAAATCCATCTTGTTGAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAACAAATTTTGAAGTGGTTGATCCAc                                                                                                                        >  2:53389/1‑141 (MQ=255)
           aaTCCATCTTGTTGAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACttgt                                                                                                                    <  1:261717/141‑1 (MQ=255)
                   ttgttgCGTATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTGAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTAtt                                                                                                            <  2:167251/141‑1 (MQ=255)
                     gttgAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGCTTACCATTTGTTTTCGCAAGTGTTCCAGCATTATCACGCTTTAACGGTAGTTGTGGGTTTAAATTAATTTGGAGTGGTTGATCCACTTGTTGCTTAttag                                                                                                          >  2:287842/1‑139 (MQ=255)
                      ttgAGTATTGTTTCATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTTGCTAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGc                                                                                                         <  2:227291/141‑1 (MQ=255)
                      ttgAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGc                                                                                                         <  1:3695/141‑1 (MQ=255)
                        gAGCTTTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCAt                                                                                                       >  2:238739/1‑141 (MQ=255)
                         aGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCAtt                                                                                                      <  1:299166/141‑1 (MQ=255)
                                tttAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAACTATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTc                                                                                               <  1:272180/141‑1 (MQ=255)
                                 ttAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCa                                                                                              >  1:136563/1‑141 (MQ=255)
                                      gCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATAcc                                                                                         >  2:244291/1‑140 (MQ=255)
                                        aTTCGATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACAtt                                                                                       <  1:108163/141‑1 (MQ=255)
                                            aaTTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTtca                                                                                   >  1:42802/1‑141 (MQ=255)
                                            aaTTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTtca                                                                                   >  1:9256/1‑141 (MQ=255)
                                               tGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTtcagca                                                                                >  2:339775/1‑141 (MQ=255)
                                                  tCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTtcagcatca                                                                             >  1:330552/1‑141 (MQ=255)
                                                   cGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTtcagcatcac                                                                            >  2:272465/1‑140 (MQ=255)
                                                          aTGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTACAATTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGc                                                                     >  1:217184/1‑141 (MQ=255)
                                                           tGTTTACCATTTTTTTTAGCATGTGCTACACGTTCATCACCATTTAATGCTTGTTGTGCTTTTAAAATATTTTGAAGTGGTTGATCCTCTTGTTTCTTATTCGCATTTTTTTTCAATACATTTTCAGCATCAGCAATAGCt                                                                    <  2:131703/141‑1 (MQ=255)
                                                           tGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCCTGTTTTGCACTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATTAGCAATAGCt                                                                    <  2:169986/141‑1 (MQ=255)
                                                                 ccATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAGTATTTTGAAGTGGTTGATCCACTTGTTGCTAATTCGCCTTGGGATTGAATAGATTTTCTGCATCAGCAATAGCTTGtttt                                                              >  2:155251/1‑140 (MQ=255)
                                                                     ttGTTTTAGCTAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAg                                                          <  2:165439/141‑1 (MQ=255)
                                                                           tAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATATAGCAGTGGTTGATCCACTTGTTGCTTGTTCGCATTTTGTTTCAATACGTTTTCAGCATCCGCAATAGCTTGTTTATAAGCAtttt                                                    >  1:149262/1‑141 (MQ=255)
                                                                            aGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTg                                                   >  1:279125/1‑141 (MQ=255)
                                                                                    cTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAGTATCGTCAGGCGGGTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTg                                           <  1:111587/141‑1 (MQ=255)
                                                                                              atcaCCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTtg                                 <  1:81368/141‑1 (MQ=255)
                                                                                              atcaCCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTtg                                 <  1:341004/141‑1 (MQ=255)
                                                                                                caCCATTTAATGCTTGTTTTGCATTTAAAATATTTTGACGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTtgtg                               >  2:252854/1‑141 (MQ=255)
                                                                                                caCCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTCTTCGCATTTTGTTTCAATACATTTTCAGCATCGGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTggtt                               >  2:224932/1‑140 (MQ=255)
                                                                                                caCCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTtgtg                               <  1:315754/141‑1 (MQ=255)
                                                                                                          tggttGTTTTGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTGCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTAc                     <  2:10082/138‑1 (MQ=255)
                                                                                                              ttttttTCATTTAAAATATTTTTATTTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTACAGtt                 <  2:150495/139‑1 (MQ=255)
                                                                                                                   tGCATTTAAAATATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTACAGTTTGCTc            <  1:142811/141‑1 (MQ=255)
                                                                                                                            aaTATTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTACAGTTTGCTCAACGTTAGc   <  1:300869/141‑1 (MQ=255)
                                                                                                                             atatTTTGAAGTGGTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTACAGTTTGCTCAACGTTAGCa  >  2:328467/1‑141 (MQ=255)
                                                                                                                                          |                                                                                                                               
TGCGACCTTTAAATCCATCTTGTTGAGCATTGTTTAATGCATTCAATTGGTCGATGTCATGTTTACCATTTGTTTTAGCAAGTGCTACACGTTCATCACCATTTAATGCTTGTTTTGCATTTAAAATATTTTGAAGTGCTTGATCCACTTGTTGCTTATTCGCATTTTGTTTCAATACATTTTCAGCATCAGCAATAGCTTGTTTATAAGCATTTTGTTTATCTGAATCTGCTTGTGTGTAATCTACAGTTTGCTCAACGTTAGCA  >  USA300TCH1516_ALE/1474501‑1474766

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: ‑