Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,137,180	C→G	A160P (GCA→CCA)	yijF ←	DUF1287 family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,137,180	0	C	G	95.1%	283.2 / 5.1	81	A160P (GCA→CCA)	yijF	DUF1287 family protein
Reads supporting (aligned to +/- strand):  ref base C (1/3);  new base G (37/40);  total (38/43)
Fisher's exact test for biased strand distribution p-value = 6.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.95e-01

CACATCTTCTTCCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGCCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATGGCGGCTAAACCA  >  NC_000913/4137088‑4137276                                                                                             |                                                                                                 cacaTCTTCTTCCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCg                                                                                           >  2:1636105/1‑100 (MQ=255) cacaTCTTCTTCCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCg                                                                                           <  2:354675/100‑1 (MQ=255) cacaTCTTCTTCCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCg                                                                                           <  1:2043387/100‑1 (MQ=255)  acaTCTTCTTCCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGt                                                                                          >  2:1670650/1‑100 (MQ=255)    aTCTTCTTCCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTa                                                                                        <  2:805877/100‑1 (MQ=255)      cttcttCCTGCGCGCCTGCGCCACTGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCACTATGTGGCAGCCCGTTATc                                                                                      >  2:1778500/1‑100 (MQ=255)      cttcttCCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATc                                                                                      >  1:1102077/1‑100 (MQ=255)      cttcttCCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATc                                                                                      <  2:1027808/100‑1 (MQ=255)       ttcttcCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATcn                                                                                     <  2:1992653/100‑2 (MQ=255)         cttcCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAg                                                                                   <  1:1032999/100‑1 (MQ=255)           tcCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTc                                                                                 >  1:1550502/1‑100 (MQ=255)           tcCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTc                                                                                 >  1:1301661/1‑100 (MQ=255)           tcCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTc                                                                                 >  1:1991917/1‑100 (MQ=255)           tcCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTc                                                                                 <  2:853247/100‑1 (MQ=255)            ccTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCg                                                                                <  2:714387/100‑1 (MQ=255)            ccTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCg                                                                                >  1:21882/1‑100 (MQ=255)               atctgcCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCa                                                                             <  1:672764/96‑1 (MQ=255)                   gcCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCaagat                                                                         >  2:672763/1‑96 (MQ=255)                     cTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGAc                                                                       <  2:1659230/100‑1 (MQ=255)                      tGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACa                                                                      >  1:1189/1‑100 (MQ=255)                        cgcCAATGTTATGTATCACCGGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCGCAATATGTGCCAGCCCGTTATCCAGTCGCCAGGAGACAat                                                                    <  2:312899/100‑1 (MQ=255)                        cgcCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAat                                                                    >  2:1222058/1‑100 (MQ=255)                        cgcCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAat                                                                    >  1:733881/1‑100 (MQ=255)                        cgcCAATATTAGGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATAAGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAat                                                                    >  2:1230186/1‑100 (MQ=255)                         gcCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGAc                                                                       <  2:603997/96‑1 (MQ=255)                          ccAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAatat                                                                  <  2:542279/100‑1 (MQ=255)                          ccAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAatat                                                                  >  1:2211782/1‑100 (MQ=255)                          ccAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAatat                                                                  >  2:489178/1‑100 (MQ=255)                             aTGTGATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGc                                                               <  1:749722/100‑1 (MQ=255)                               gTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGccc                                                             >  1:382584/1‑100 (MQ=255)                                ttATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCg                                                            >  1:2192970/1‑100 (MQ=255)                                  aTGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCt                                                          <  1:11350/100‑1 (MQ=255)                                    gTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTg                                                        >  2:84064/1‑100 (MQ=255)                                      aTCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGAt                                                      <  1:1209664/100‑1 (MQ=255)                                       tCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATa                                                     <  1:2333516/100‑1 (MQ=255)                                       tCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATa                                                     <  2:1301658/100‑1 (MQ=255)                                        cACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAg                                                    >  2:234606/1‑100 (MQ=255)                                        cACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAg                                                    <  1:1776171/100‑1 (MQ=255)                                         aCCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGt                                                   >  2:1237851/1‑100 (MQ=255)                                         aCCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGCCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGt                                                   >  1:860389/1‑100 (MQ=255)                                          ccAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGtn                                                  <  2:733880/100‑2 (MQ=255)                                           cAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTc                                                  >  1:180364/1‑99 (MQ=255)                                           cAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGCCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTcn                                                 <  2:860387/100‑2 (MQ=255)                                              cggcgTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGCCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTg                                              <  1:2183905/100‑1 (MQ=255)                                               ggcgTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTgg                                             >  2:1199572/1‑100 (MQ=255)                                                  gTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGt                                          <  2:2330109/100‑1 (MQ=255)                                                  gTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGt                                          <  1:84066/100‑1 (MQ=255)                                                     ccGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCt                                       >  2:998336/1‑100 (MQ=255)                                                      cGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCtt                                      >  1:923783/1‑100 (MQ=255)                                                       gTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTg                                     >  1:1891425/1‑100 (MQ=255)                                                        tCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGc                                    <  1:1237854/100‑1 (MQ=255)                                                        tCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGc                                    <  2:21881/100‑1 (MQ=255)                                                         cgcgGGCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCt                                   <  2:1661073/100‑1 (MQ=255)                                                             ggCGAAGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCtggtg                               >  1:679309/1‑100 (MQ=255)                                                                  aGCCATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGGCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCg                          <  1:1778505/100‑1 (MQ=255)                                                                     cATCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCgtgt                       >  1:981646/1‑100 (MQ=255)                                                                       tCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGttt                     >  1:656377/1‑100 (MQ=255)                                                                       tCTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGttn                     <  2:2077731/100‑2 (MQ=255)                                                                        cTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGtttt                    <  2:1590282/100‑1 (MQ=255)                                                                        cTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGtttt                    <  2:1102075/100‑1 (MQ=255)                                                                        cTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGtttt                    <  2:2054025/100‑1 (MQ=255)                                                                        cTGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGttt                     <  2:416135/99‑1 (MQ=255)                                                                         tGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTa                   >  1:1139152/1‑100 (MQ=255)                                                                         tGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTa                   <  1:1975172/100‑1 (MQ=255)                                                                         tGAAACCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTa                   <  2:251009/100‑1 (MQ=255)                                                                           aaaCCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGGGTGGCGTGTTTTATc                 >  2:191753/1‑100 (MQ=255)                                                                            aaCCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCa                <  2:1189/100‑1 (MQ=255)                                                                            aaCCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCa                >  1:1674070/1‑100 (MQ=255)                                                                            aaCCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCa                >  1:1674147/1‑100 (MQ=255)                                                                            aaCCACCCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTAGATAATCACTGGCGTGCTTGATGGTGGGGCgtctgctgagc                >  2:2090072/1‑91 (MQ=255)                                                                               caccCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATgg             <  2:662123/100‑1 (MQ=255)                                                                               caccCCAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATgg             >  1:662124/1‑100 (MQ=255)                                                                                 ccccAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATggcg           >  2:2232632/1‑100 (MQ=255)                                                                                   ccAATATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATggcggc         >  1:1219560/1‑100 (MQ=255)                                                                                     aaTATGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATGGCGGCTa       <  2:180362/100‑1 (MQ=255)                                                                                      atatGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATGGCGGCTaa      <  2:1674142/100‑1 (MQ=255)                                                                                      atatGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATGGCGGCTaa      <  2:1674065/100‑1 (MQ=255)                                                                                       tatGTGGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATGGCGGCTaaa     <  2:1139150/100‑1 (MQ=255)                                                                                         tgtgGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATGGCGGCTAAAcc   <  1:1670655/100‑1 (MQ=255)                                                                                         tgtgGCAGCCCGTGATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATGGCGGCTAAAcc   <  1:191755/100‑1 (MQ=255)                                                                                          gtgGCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATGGCGGCTAAACCa  >  2:357908/1‑100 (MQ=255)                                                                                             |                                                                                                 CACATCTTCTTCCTGCGCGCCTGCGCCAATGTTATGTATCACCAGCGGCGTACCGTCGCGGGCGAAGCCATCTGAAACCACCCCAATATGTGCCAGCCCGTTATCCAGTCGCCAGGAGACAATATCGCCCGCTTGATAGTCACTGGGGTTCTTGCTGGTGGGGCGTGTTTTATCATGGCGGCTAAACCA  >  NC_000913/4137088‑4137276

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: ‑