Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	AP009048	281,512	C→T	11.8%	S11F (TCC→TTC)	yagE →	predicted lyase/synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AP009048	281,512	0	C	T	11.8%	170.6 / 11.0	59	S11F (TCC→TTC)	yagE	predicted lyase/synthase
Reads supporting (aligned to +/- strand):  ref base C (25/27);  new base T (3/4);  total (28/31)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TAAATAAACGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATAA  >  AP009048/281445‑281578                                                                    |                                                                   taaataaaGGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCcgc                                                                 >  1:3613322/1‑71 (MQ=255) taaataaaCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCcgc                                                                 >  1:1691631/1‑71 (MQ=255) taaataaaCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCcgc                                                                 >  1:2919167/1‑71 (MQ=255)  aaataaaCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCcgcg                                                                >  1:3197224/1‑71 (MQ=255)   aataaaCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCcgc                                                                 <  1:1080154/69‑1 (MQ=255)    ataaaCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCACAGTTCGCgtt                                                              <  1:1421026/71‑1 (MQ=255)      aaaCGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCgt                                                               <  1:3908911/68‑1 (MQ=255)             cgCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCgttgtt                                                           >  1:3626228/1‑65 (MQ=255)             cgCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACgg                                                      >  1:331308/1‑70 (MQ=255)               cTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGaa                                                   <  1:155668/71‑1 (MQ=255)                tGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTTCGCGTTGTTCACgg                                                      >  1:885957/1‑67 (MQ=255)                 gTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTTCGCgttg                                                             <  1:3351979/59‑1 (MQ=255)                  ttCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTTCGCGTTGTTCACGGGAAt                                                  <  1:1845406/69‑1 (MQ=255)                  ttCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTTCGCGTTGTTCACGGGAATc                                                 >  1:1859998/1‑70 (MQ=255)                  ttCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAAt                                                  <  1:1046932/69‑1 (MQ=255)                  ttCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAAt                                                  <  1:2054795/69‑1 (MQ=255)                  ttCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCa                                                >  1:2507916/1‑71 (MQ=255)                  ttCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCa                                                <  1:933432/71‑1 (MQ=255)                   tCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCgttgt                                                            <  1:4102343/58‑1 (MQ=255)                    cTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCAtt                                              >  1:2138297/1‑71 (MQ=255)                       taATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTccc                                           >  1:1423088/1‑71 (MQ=255)                       taATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTccc                                           >  1:2401955/1‑71 (MQ=255)                       taATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTc                                             <  1:4372927/69‑1 (MQ=255)                            tAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTc                                                          <  1:355348/51‑1 (MQ=255)                             aGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGtc                                     >  1:2155554/1‑71 (MQ=255)                               aaCAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAAt                                                  <  1:1452464/56‑1 (MQ=255)                                aCAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTTCGCGTTGTTCa                                                         >  1:139529/1‑48 (MQ=255)                                 cAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAAt                                                  <  1:2820654/54‑1 (MQ=255)                                  aaaaTGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTccac                                <  1:4189523/71‑1 (MQ=255)                                   aaaTGATTCAGCAAGGAGATCTCATGCCGCAGTCcg                                                                  >  1:2642190/1‑36 (MQ=255)                                    aaTGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCgttgtt                                                           >  1:95657/1‑42 (MQ=255)                                     aTGATTCAGCAAGGAGATCTCATGCCGGAGTCCGCGTTGTTCACGGGAAt                                                  >  1:2591264/1‑50 (MQ=255)                                     aTGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCAt                             <  1:2199629/71‑1 (MQ=255)                                     aTGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCAt                             <  1:717815/71‑1 (MQ=255)                                        aTTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCAttt                           <  1:740884/70‑1 (MQ=255)                                         ttCAGCAAGGAGATCTCATGCCGCAGTCCGCgttgtt                                                           <  1:70920/37‑1 (MQ=255)                                         ttCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCAttttt                         <  1:1568424/71‑1 (MQ=255)                                         ttCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCAttttt                         <  1:904761/71‑1 (MQ=255)                                           cAGCAACGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTa                        <  1:4497144/70‑1 (MQ=255)                                            aGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTAc                       <  1:4072785/70‑1 (MQ=255)                                              cAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCAc                                                        <  1:3076705/35‑1 (MQ=255)                                               aaGGAGATCTCATGCCGCAGTTCGCGTTGTTCACgg                                                      <  1:1412345/36‑1 (MQ=255)                                                      tctcATGCCGCAGTCCGCGTTGTTCACGGGAATCATTccccc                                         >  1:1002903/1‑42 (MQ=255)                                                       ctcATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGt                                      >  1:1283736/1‑44 (MQ=255)                                                       ctcATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGt                                      >  1:724924/1‑44 (MQ=255)                                                       ctcATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCAttt                           <  1:1632184/55‑1 (MQ=255)                                                       ctcATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACg               >  1:4493222/1‑67 (MQ=255)                                                       ctcATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGc             >  1:1540384/1‑69 (MQ=255)                                                        tcATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAg          >  1:3835540/1‑71 (MQ=255)                                                         cATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGc         >  1:4130962/1‑71 (MQ=255)                                                          aTGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGcc            >  1:1003678/1‑67 (MQ=255)                                                          aTGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCt        >  1:1951829/1‑71 (MQ=255)                                                           tGCAGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTATTACCGCCGACGGCCAGCt        >  1:3365158/1‑70 (MQ=255)                                                             ccGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCg      <  1:3168566/70‑1 (MQ=255)                                                             ccGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGa     <  1:31751/71‑1 (MQ=255)                                                              cGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGa     >  1:364107/1‑70 (MQ=255)                                                                cAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATaa  <  1:4422964/71‑1 (MQ=255)                                                                   tCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTcca                                 <  1:2282677/37‑1 (MQ=255)                                                                   tCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCAttt                           <  1:3408091/43‑1 (MQ=255)                                                                    |                                                                   TAAATAAACGAACGCTGTTCTATAATGTAGAACAAAATGATTCAGCAAGGAGATCTCATGCCGCAGTCCGCGTTGTTCACGGGAATCATTCCCCCTGTCTCCACCATTTTTACCGCCGACGGCCAGCTCGATAA  >  AP009048/281445‑281578

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑