Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,773,033 C→T 12.1% C423Y (TGT→TAT)  hemA ← Glutamyl‑tRNA reductase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,773,0330CT12.1% 76.6 / 2.1 33C423Y (TGT→TAT) hemAGlutamyl‑tRNA reductase
Reads supporting (aligned to +/- strand):  ref base C (13/16);  new base T (2/2);  total (15/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.11e-01

AATTTCATTGAATCGAATAAACAGGTTTTCTTGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCTTTCAACATTTGATTGATGATACTTTTTGTATG  >  USA300TCH1516_ALE/1772897‑1773160
                                                                                                                                        |                                                                                                                               
aatTTCATTGAATCGAATAAACAGGTTTTCTTGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTc                                                                                                                             <  2:317698/141‑1 (MQ=255)
 atTTCATTGAATCGAATAAACAGGTTTTCTTGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACTTTCa                                                                                                                            >  1:238830/1‑141 (MQ=255)
          aaTCGAATAAACAGGTTTTCTTGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGATATTCAGCTTCGatt                                                                                                                   >  2:89959/1‑140 (MQ=255)
          aaTCGAATAAACAGGTTTTCTTGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGATATTCAGCTTCGata                                                                                                                   >  2:89958/1‑141 (MQ=255)
           aTCGAATAAACAGTCTTTCTTGCATAGTAACACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGACATTTCCTTCACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGatat                                                                                                                  <  2:340809/141‑1 (MQ=255)
             cGAATAAACAGGTTTTCTTGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCa                                                                                                                <  2:276392/141‑1 (MQ=255)
                  aaaCAGGTTTTCTTGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAatat                                                                                                           >  1:370499/1‑141 (MQ=255)
                  aaaCAGGTTTTCTTGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAatat                                                                                                           <  2:253486/141‑1 (MQ=255)
                       ggTTTTCTTGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCCGCTTCGATATCAAATATAtttt                                                                                                      >  1:11998/1‑141 (MQ=255)
                            tCTTGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAAt                                                                                                 >  1:23956/1‑141 (MQ=255)
                            tCTTGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAAt                                                                                                 >  1:40259/1‑141 (MQ=255)
                              ttGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAg                                                                                               <  2:51916/141‑1 (MQ=255)
                                                 tAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACtt                                                                            <  1:292192/141‑1 (MQ=255)
                                                           aTTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTTTTATCac                                                                  >  2:58995/1‑141 (MQ=255)
                                                            ttCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATCTCAAATATATTTTGAAATAGCTCTAATTTTTCATCACTTTTCTTCTCact                                                                 >  2:122989/1‑141 (MQ=255)
                                                             tCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCacta                                                                <  2:11998/141‑1 (MQ=255)
                                                                  aCTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTaa                                                           <  2:12972/141‑1 (MQ=255)
                                                                          tACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTgg                                                   <  2:23956/141‑1 (MQ=255)
                                                                           aCGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGATATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGc                                                  <  1:89959/141‑1 (MQ=255)
                                                                           aCGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGATATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGc                                                  <  1:89958/141‑1 (MQ=255)
                                                                                     gAAATTTCCTTGACCTAGCTTTCTTTTTGTTGCGTCGCTTGCGCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTATTTGTCCTGTTTAATa                                        >  2:217418/1‑141 (MQ=255)
                                                                                               tGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCCTTCa                              >  1:83406/1‑141 (MQ=255)
                                                                                                 aCCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCTTTCAAc                            >  1:46722/1‑141 (MQ=255)
                                                                                                     tGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAGATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCTTTCAACAttt                        <  2:66740/141‑1 (MQ=255)
                                                                                                          tctttTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATCTATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCTTTCAACATtttattg                   >  2:61593/1‑141 (MQ=255)
                                                                                                          tctttTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCTTTCAACATttgattg                   >  2:129192/1‑141 (MQ=255)
                                                                                                             ttttGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCTTTCAACATTTGATtgatg                >  2:47951/1‑141 (MQ=255)
                                                                                                             ttttGTTGCGTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCTTTCAACATTTGATtgatg                <  1:361587/141‑1 (MQ=255)
                                                                                                               tagtttCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCTTTCAACATTTGATTgatgat              <  2:374326/139‑1 (MQ=255)
                                                                                                                 gttgCTCCGCTTCCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCTTTCAACATTTGATTGATGATAc            <  1:58669/141‑1 (MQ=255)
                                                                                                                    gCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCTTTCAACATTTGATTGATGATACttt         <  1:342077/141‑1 (MQ=255)
                                                                                                                     cTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTCTGAAATATCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCTTTCAACATTTGATTGATGATACtttt        <  1:193249/141‑1 (MQ=255)
                                                                                                                           ttGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCATAGGGTTGTGTAATAGGATCTTTCAACATTTGATTGATGATACTTTTTGTATg  <  1:332732/141‑1 (MQ=255)
                                                                                                                                        |                                                                                                                               
AATTTCATTGAATCGAATAAACAGGTTTTCTTGCATATTATCACCATATTAATATGCTTATTCAAAACTAAAGATACGTCGCGCTGAAATTTCCTTGACCTTGCTTTCTTTTTGTTGCTTCGCTTGCTCATGAGGACATTCAGCTTCGATATCAAATATATTTTGAAATAGCTCTAATTTTTCATTACTTTTCTTATCACTACTTAATTCTTTGGCCTGTTTAATAGGATCTTTCAACATTTGATTGATGATACTTTTTGTATG  >  USA300TCH1516_ALE/1772897‑1773160

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: ‑