Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,638,727 C→T 8.7% D240N (GAT→AAT)  xylB ← Xylulose kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,638,7270CT 8.7% 141.6 / 4.7 46D240N (GAT→AAT) xylBXylulose kinase
Reads supporting (aligned to +/- strand):  ref base C (25/17);  new base T (2/2);  total (27/19)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

TAAGACATAACAAAATATTCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCAACATTTCCTTGGAAATACCCAGCAGTTCTAATGCC  >  USA300TCH1516_ALE/2638587‑2638866
                                                                                                                                            |                                                                                                                                           
tAAGACATAACAAAATATTCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATc                                                                                                                                             <  1:291346/141‑1 (MQ=255)
tAAGACATAACAAAATATTCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATc                                                                                                                                             <  1:169966/141‑1 (MQ=255)
 aaGACATAACAAAATATTCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCa                                                                                                                                            >  1:411678/1‑141 (MQ=255)
 aaGACATAACAAAATATTCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCa                                                                                                                                            >  1:351624/1‑141 (MQ=255)
 aaGACATAACAAAATATTCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCa                                                                                                                                            >  1:199592/1‑141 (MQ=255)
 aaGACATAACAAAATATTCTACCTTTGTAATCAGAACGCGTGATATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCa                                                                                                                                            >  2:252726/1‑141 (MQ=255)
  aGACATAACAAAATATTCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCAc                                                                                                                                           >  1:237749/1‑141 (MQ=255)
     cATAACAAAATATTCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCg                                                                                                                                        <  1:115563/141‑1 (MQ=255)
           aaaaTATTCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCaa                                                                                                                                  >  2:402562/1‑141 (MQ=255)
               tatTCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAAc                                                                                                                              >  1:311537/1‑141 (MQ=255)
                 ttCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACaa                                                                                                                            >  1:229874/1‑141 (MQ=255)
                  tCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGAGCACTAAATTAGAAAGGACCCCATCACTCGCACCAATAACaaa                                                                                                                           >  1:120891/1‑141 (MQ=255)
                   cTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCGCTCGCACCAATAACAAAc                                                                                                                          <  2:192606/141‑1 (MQ=255)
                   cTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAAc                                                                                                                          <  2:367474/141‑1 (MQ=255)
                         ttGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTa                                                                                                                    <  1:222082/141‑1 (MQ=255)
                                cAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATTACTCGCACCAATAACAAACGGTGTATCTttat                                                                                                             >  1:170850/1‑141 (MQ=255)
                                cAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATTACTCGCACCAATAACAAACGGTGTATCTttat                                                                                                             >  1:199365/1‑141 (MQ=255)
                                 aGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTttatt                                                                                                            >  1:360490/1‑141 (MQ=255)
                                  gTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTttatta                                                                                                           <  2:293153/141‑1 (MQ=255)
                                    aCGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAg                                                                                                         >  1:437742/1‑141 (MQ=255)
                                       cgGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGccc                                                                                                      >  2:389710/1‑141 (MQ=255)
                                         gTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCa                                                                                                    >  1:28549/1‑141 (MQ=255)
                                               ctatcACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATg                                                                                              >  2:13192/1‑141 (MQ=255)
                                                     caGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCAt                                                                                        <  1:218151/141‑1 (MQ=255)
                                                        tACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAAc                                                                                     >  2:259271/1‑141 (MQ=255)
                                                          cGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGt                                                                                   >  1:122899/1‑141 (MQ=255)
                                                           gAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGtt                                                                                  <  2:134395/141‑1 (MQ=255)
                                                                  cccAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCAt                                                                           <  1:169138/141‑1 (MQ=255)
                                                                  cccAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCAt                                                                           <  1:379312/141‑1 (MQ=255)
                                                                             cGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATTACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTtcatca                                                                <  2:170850/141‑1 (MQ=255)
                                                                             cGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATTACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTtcatca                                                                <  2:199365/141‑1 (MQ=255)
                                                                               aTTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATcaca                                                              <  1:11568/141‑1 (MQ=255)
                                                                                   tgACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACg                                                          >  1:16876/1‑141 (MQ=255)
                                                                                             ttCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAAc                                                >  1:98548/1‑141 (MQ=255)
                                                                                             ttCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAAc                                                >  2:232383/1‑141 (MQ=255)
                                                                                                       ccAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGc                                      <  2:76113/141‑1 (MQ=255)
                                                                                                         aaCACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCaa                                    >  2:260045/1‑141 (MQ=255)
                                                                                                           cacTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCAACa                                  <  2:199592/141‑1 (MQ=255)
                                                                                                           cacTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCAACa                                  <  1:252726/141‑1 (MQ=255)
                                                                                                                         aaaTTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCAACATTTCCTTGGAAATa                    >  2:75760/1‑141 (MQ=255)
                                                                                                                                aaaGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCAACATTTCCTTGGAAATACCcagca             <  1:389710/141‑1 (MQ=255)
                                                                                                                                aaaGGACCCCAACACTCGAACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCAACCCCCACCTTGTTGCAACTCATTCAGGCAACATTTCCTTGGAAATAccccgac             <  2:459047/141‑5 (MQ=255)
                                                                                                                                   ggACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCAACATTTCCTTGGAAATACCCAGCAGtt          >  2:322802/1‑141 (MQ=255)
                                                                                                                                   ggACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCAACATTTCCTTGGAAATACCCAGCAGtt          <  1:169650/141‑1 (MQ=255)
                                                                                                                                        ccATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCAACATTTCCTTGGAAATACCCAGCAGTTCTAAt     >  1:333007/1‑141 (MQ=255)
                                                                                                                                        ccATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCAACATTTCCTTGGAAATACCCAGCAGTTCTAAt     >  2:419727/1‑141 (MQ=255)
                                                                                                                                          aTCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATCACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCAACATTTCCTTGGAAATACCCAGCAGTTCTAATGc   <  1:250924/141‑1 (MQ=255)
                                                                                                                                           tCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCAACATTTCCTTGGAAATACCCAGCAGTTCTAATGcc  >  2:425889/1‑141 (MQ=255)
                                                                                                                                            |                                                                                                                                           
TAAGACATAACAAAATATTCTACCTTTGTAATCAGTACGCGGTTTATCTATCACAGTACGAATCGCCCCAGATGTACCGATTGTGACAGCAACTTCTCCTTTACCAACACTATTGACACCTAAATTAGAAAGGACCCCATCACTCGCACCAATAACAAACGGTGTATCTTTATTAAGCCCCATTAATGTTGCATAACGTTCTTTCATACCTTTCATCACATACGTTGTTGGAACTAATTCCGGCAACATTTCCTTGGAAATACCCAGCAGTTCTAATGCC  >  USA300TCH1516_ALE/2638587‑2638866

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