Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,202,107	G→C	13.8%	S420S (TCG→TCC) ‡	sdaA →	L‑serine deaminase I

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,202,107	0	G	C	13.8%	263.9 / 23.8	94	S420S (TCG→TCC) ‡	sdaA	L‑serine deaminase I
Reads supporting (aligned to +/- strand):  ref base G (37/44);  new base C (3/10);  total (40/54)
Fisher's exact test for biased strand distribution p-value = 1.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.25e-01

CCATTGCCTCTGTGAAGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCAAATACCGCGAAACCTCA  >  minE/1202037‑1202176                                                                       |                                                                      ccATTGCCTCTGTGAAGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCg                                                                       >  1:2211402/1‑71 (MQ=255)   aTTGCCTCTGTGAAGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCg                                                                       <  1:845554/69‑1 (MQ=255)     tGCCTCTGTGAAGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTg                                                                    >  1:3480006/1‑70 (MQ=255)     tGCCTCTGTGAAGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTg                                                                    >  1:611908/1‑70 (MQ=255)          ctGTGAAGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAg                                                              >  1:4823271/1‑71 (MQ=255)          ctGTGAAGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAg                                                              >  1:4865052/1‑71 (MQ=255)           tgtgAAGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAgg                                                             >  1:4900608/1‑71 (MQ=255)           tgtgAAGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAgg                                                             >  1:3969631/1‑71 (MQ=255)           tgtgAAGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAgg                                                             >  1:1298988/1‑71 (MQ=255)             tgAAGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTc                                                           <  1:3333494/71‑1 (MQ=255)               aaGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCa                                                          >  1:1598500/1‑70 (MQ=255)               aaGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCAt                                                         <  1:1483214/71‑1 (MQ=255)                aGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATc                                                        <  1:1486707/71‑1 (MQ=255)                   cGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGaa                                                     <  1:1098307/71‑1 (MQ=255)                   cGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGaa                                                     <  1:1944295/71‑1 (MQ=255)                      ttAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAAc                                                   >  1:3092243/1‑70 (MQ=255)                       tAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGa                                                 >  1:573100/1‑71 (MQ=255)                        aaCGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGa                                                 <  1:2635090/70‑1 (MQ=255)                        aaCGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGAt                                                >  1:4061821/1‑71 (MQ=255)                        aaCGCCGCACGTATGGCGCTGCGCCGTACCAGCGAGCCGCGCGTCTGCCTCGATAAAGTTATCGAAAcca                                                 >  1:1675178/1‑68 (MQ=9)                        aaCGCCGCACGTATGGCGCTGCGCCGTACCAGCGAGCCGCGCGTCTGCCTCGATAAAGTTATCGAAAcca                                                 <  1:2338470/70‑3 (MQ=9)                        aaCGCCGCACGTATGGCGCTGCGCCGTACCAGCGAGCCGCGCGTCTGCCTCGATAAAGTTATCGAAAcca                                                 <  1:2331851/70‑3 (MQ=9)                         aCGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGAt                                                <  1:5636342/70‑1 (MQ=255)                         aCGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGAt                                                <  1:1416027/70‑1 (MQ=255)                         aCGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATg                                               <  1:214850/71‑1 (MQ=255)                         aCGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATg                                               >  1:1591409/1‑71 (MQ=255)                          cgccgcGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAAc                                                   <  1:1318944/66‑1 (MQ=255)                            ccgcGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGa                                                 >  1:2896731/1‑66 (MQ=255)                             cgcacgTATGGCGCTGCGCCGTACCAGCGAGCCGCGCGTCTGCCTCGATAAAGTTATCGAAACCATGTACg                                           <  1:2094673/71‑1 (MQ=12)                              gcgcgGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGa                                          <  1:3272937/71‑1 (MQ=255)                                 cgtaTGGCGCTGCGCCGTACCAGCGAGCCGCGCGTCTGCCTCGATAAAGTTATCGAAACCATGTACGAAAc                                       <  1:3611663/68‑1 (MQ=12)                                   gATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCg                                     >  1:3287383/1‑71 (MQ=255)                                      ggCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGt                                   >  1:1703545/1‑70 (MQ=255)                                       gCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTa                                  <  1:5028452/70‑1 (MQ=255)                                       gCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTa                                  <  1:374468/70‑1 (MQ=255)                                       gCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTa                                  <  1:602788/70‑1 (MQ=255)                                        ctctGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCg                                                       <  1:1429092/48‑1 (MQ=255)                                         gctGCGCCGTACCAGCGAGCCGCGCGTCTGCCTCGATAAAGTTATCGAAACCATGTACGAAACAGGTaaag                               <  1:3752269/70‑3 (MQ=12)                                         gctGCGCCGTACCAGCGAGCCGCGCGTCTGCCTCGATAAAGTTATCGAAACCATGTACGAAACAGGTaaag                               <  1:155195/70‑3 (MQ=12)                                          ctGCGCCGTACCAGCGAGCCGCGCGTCTGCCTCGATAAAGTTATCGAAACCATGTACGAAACAGGTaa                                 >  1:1338565/1‑68 (MQ=16)                                          ctGCGCCGTACCAGCGAGCCGCGCGTCTGCCTCGATAAAGTTATCGAAACCATGTACGAAACAGGTaa                                 >  1:4658923/1‑68 (MQ=16)                                          ctGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGa                              >  1:5130055/1‑71 (MQ=255)                                           tGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTAc                                            <  1:279462/56‑1 (MQ=255)                                           tGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTAc                                            <  1:5138410/56‑1 (MQ=255)                                             cgccgtACCAGCGAGCCGCGCGTCTGCCTCGATAAAGTTATCGAAACCATGTACGAAACAGGTAAAGata                            <  1:1741280/70‑3 (MQ=9)                                             cgccgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGa                                          >  1:4681059/1‑56 (MQ=255)                                             cgccgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACAt                           <  1:5233609/71‑1 (MQ=255)                                              gccgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATg                          <  1:1053086/71‑1 (MQ=255)                                              gccgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATg                          <  1:3386637/71‑1 (MQ=255)                                              gccgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATg                          <  1:2945933/71‑1 (MQ=255)                                               ccgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGa                         <  1:740483/71‑1 (MQ=255)                                               ccgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGa                         <  1:3133687/71‑1 (MQ=255)                                               ccgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGa                         <  1:2237289/71‑1 (MQ=255)                                               ccgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGa                         <  1:485031/71‑1 (MQ=255)                                                cgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGaaa                                                    >  1:1721249/1‑43 (MQ=255)                                                cgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGaaa                                                    >  1:4772866/1‑43 (MQ=255)                                                cgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATg                          <  1:122387/69‑1 (MQ=255)                                                cgcACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGaa                        >  1:2482802/1‑71 (MQ=255)                                                  cACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACg                      >  1:3152718/1‑71 (MQ=255)                                                  cACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACg                      >  1:2128450/1‑71 (MQ=255)                                                    ccAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGcc                    <  1:2282120/71‑1 (MQ=255)                                                    ccAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGcc                    <  1:1873247/71‑1 (MQ=255)                                                     cAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGcc                    >  1:4645873/1‑70 (MQ=255)                                                      aGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTa                                             >  1:3994514/1‑44 (MQ=255)                                                       gTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCaaa                 <  1:5386880/71‑1 (MQ=255)                                                       gTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCaaa                 <  1:2388045/71‑1 (MQ=255)                                                        tGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCAAAt                <  1:3202003/71‑1 (MQ=255)                                                         gCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCAAATa               >  1:1085806/1‑71 (MQ=255)                                                          cACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCAAATa               <  1:588897/70‑1 (MQ=255)                                                           gccGCGCGTCTGCCTCGATAAAGTTATCGAAACCATGTACGAAACAGGTAAAGATATg                          <  1:4211468/57‑1 (MQ=2)                                                           gccGCGCGTCTGCCTCGATAAAGTTATCGAAACCATGTACGAAACAGGTAAAGATATg                          <  1:5078341/57‑1 (MQ=2)                                                           gccGCGCGTCTGCCTCGATAAAGTTATCGAAACCATGTACGAAACAGGTAAAGATATg                          <  1:3728018/57‑1 (MQ=2)                                                            ccGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGa                         >  1:852721/1‑58 (MQ=255)                                                            ccGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGa                         >  1:2673068/1‑58 (MQ=255)                                                            ccGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGa                         >  1:5550167/1‑58 (MQ=255)                                                            ccGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCa                   <  1:2307687/64‑1 (MQ=255)                                                               cgcgTCTCGCTGGATAAGGTCATCGAAACGATGTACGaaa                                        >  1:5416344/1‑40 (MQ=255)                                                               cgcgTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCAAATACcgcg          >  1:2217578/1‑70 (MQ=255)                                                               cgcgTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCAAATACcgcg          >  1:3409604/1‑70 (MQ=255)                                                               cgcgTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCAAATACCGCGa         <  1:4482551/71‑1 (MQ=255)                                                               cgcgTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCAAATACCGCGa         <  1:4411502/71‑1 (MQ=255)                                                               cgcgTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCAAATACCGCGa         <  1:3744168/71‑1 (MQ=255)                                                                   tctcGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCAAATACcgc           <  1:5520954/65‑1 (MQ=255)                                                                    ctcGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAg                                <  1:4255399/43‑1 (MQ=255)                                                                    ctcGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGaa                        >  1:222754/1‑51 (MQ=255)                                                                    ctcGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGaa                        >  1:3029786/1‑51 (MQ=255)                                                                    ctcGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCa                   <  1:453443/56‑1 (MQ=255)                                                                    ctcGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCa                   <  1:584898/56‑1 (MQ=255)                                                                    ctcGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCa                   <  1:3526690/56‑1 (MQ=255)                                                                    ctcGCTGGATAAGGTCATCGAAACGATGCACGAAACCGGTAAg                                <  1:5162626/43‑1 (MQ=255)                                                                     tcGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAgg                               <  1:5378160/43‑1 (MQ=255)                                                                     tcGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCaaa                 >  1:3928558/1‑57 (MQ=255)                                                                     tcGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCaa                  >  1:2460716/1‑56 (MQ=255)                                                                      cGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAgg                               <  1:1468633/42‑1 (MQ=255)                                                                      cGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGa                              >  1:5576121/1‑43 (MQ=255)                                                                      cGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCAAATACCGCGAAACCTCa  >  1:4829874/1‑71 (MQ=255)                                                                       gCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGa                              <  1:438422/42‑1 (MQ=255)                                                                       |                                                                      CCATTGCCTCTGTGAAGGCGATTAACGCCGCGCGGATGGCTCTGCGCCGCACCAGTGCACCGCGCGTCTCGCTGGATAAGGTCATCGAAACGATGTACGAAACCGGTAAGGACATGAACGCCAAATACCGCGAAACCTCA  >  minE/1202037‑1202176

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑