Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_007779	3,777,741	G→T	20.2%	L310F (TTG→TTT)	Y75_RS18735 →	PTS transporter subunit EIIC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007779	3,777,741	0	G	T	20.2%	31.0 / 3.7	31	L310F (TTG→TTT)	Y75_RS18735	PTS transporter subunit EIIC
Reads supporting (aligned to +/- strand):  ref base G (8/16);  new base T (4/2);  total (12/19)
Fisher's exact test for biased strand distribution p-value = 1.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.44e-01

ACCACTTCATCTACGGACAGTTTATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGCTT‑GC‑TG‑ATTCCCGC‑AACC‑TTAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGAC  >  NC_007779/3777506‑3777974                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                accacTTCATCTACGGACAGTTTATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGACTT‑GA‑Tg                                                                                                                                                                                                                                             >  1:25515/1‑239 (MQ=255)   cacTTCATCTACGGACAGTTTATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGCTT‑GC‑TG‑At                                                                                                                                                                                                                                          <  1:567165/239‑1 (MQ=255)     cTTCATCTACGGACAGTTTATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGGGT‑GC‑TG‑ttt                                                                                                                                                                                                                                         >  1:866511/1‑238 (MQ=255)       tCATCTACGGACAGTTTATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGCTT‑GC‑TG‑ATTccc                                                                                                                                                                                                                                      <  1:1786165/239‑1 (MQ=255)                          cTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGGCT‑TC‑TGTTTTCGCCC‑ACCC‑TAAA‑CCGCCaag                                                                                                                                                                                                                 >  1:1878958/1‑237 (MQ=255)                          cTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGCTT‑TG‑TG‑GTTTCCTC‑AACC‑CTAA‑CCGcccagc                                                                                                                                                                                                                >  1:1781728/1‑235 (MQ=255)                             tGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTTCTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGCGT‑TC‑TG‑TTTCCCGC‑CACC‑CCAA‑CCCCCCTGCtgg                                                                                                                                                                                                             >  2:686099/1‑239 (MQ=255)                             tGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGGTT‑GT‑TG‑TTTTCCGC‑CACC‑CTAA‑CCCCCCAGCtgt                                                                                                                                                                                                             >  1:750591/1‑238 (MQ=255)                             tGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGCTT‑GC‑GG‑GGTCCCCC‑CCCC‑CTTA‑CCGCCacacggg                                                                                                                                                                                                             >  1:1981074/1‑233 (MQ=255)                               gTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGGTT‑TG‑TG‑ATTTCCCC‑CACC‑CTAA‑CACCCATggcgggg                                                                                                                                                                                                           >  1:1179162/1‑233 (MQ=255)                               gTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGGTT‑GC‑TG‑GTTTCCTC‑CACC‑CTAA‑CCGCCAAGGtgggg                                                                                                                                                                                                           >  1:506075/1‑237 (MQ=255)                                        cTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGCTT‑GC‑TG‑ATTCCCg                                                                                                                                                                                                                                     <  1:1150275/207‑1 (MQ=255)                                                     cATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGGGT‑GC‑TG‑ATTTCCGC‑CACC‑TTAA‑CCGCCATGCTGGTGGGGAATACCG‑AAACGCCGGGAt                                                                                                                                                                                    >  1:209787/1‑239 (MQ=255)                                                                      cgcAGCATCTGAAAGAGTTCAGTTTGAGCGCCGAGCCGCTAAAATCGTTTTTCCCGGAGGGCGT‑TTTTGCCCTGCACGGTAACTAAAAAATCTTGGGG‑GCG‑GTGGGCTTTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GGGGGGGGTTT‑GC‑TG‑ATTCCCGC‑AACC‑TTAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCAt                                                                                                                                                                    <  1:1301239/238‑1 (MQ=255)                                                                         agcaTCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGGGT‑GCTTG‑TTTCCCCC‑ACCC‑TAAA‑CCCCCCACCGGGGGGGAGTTACC‑‑AACCGCTGGCATTTACCCTCCTTTTCAtttt                                                                                                                                                                 >  2:774417/1‑237 (MQ=255)                                                                                       ttCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGCTT‑GC‑TG‑ATTccc                                                                                                                                                                                                                                      <  1:1688227/159‑1 (MQ=255)                                                                                                 gcgcCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGGTT‑GCTTG‑GTTCCCCC‑ACCC‑TAAA‑CC‑CCCTGCTCGTGGGGAGGATCGCAACGGCGGGTGTTACCCTTCCTTTTCTTTTCACCG‑TGCTTTTTTCgggtgtcgc                                                                                                                                         >  2:398282/1‑231 (MQ=255)                                                                                                          cgcgaaaaTCGTTGTTCCCGGAGGGGGT‑TTTTGCCCTGCGCGGTACCTAAAAAATCTTGGGG‑GCG‑GTGGGCATTTCTTTGGCGATGTCC‑TTCACTCCCGCCCCGAAAAATCGGTTAAAA‑GGGGCGGCTTG‑GC‑TG‑ATTCCCGC‑ACCC‑TTAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTggc                                                                                                                                <  1:1290151/233‑1 (MQ=255)                                                                                                                    gttgtcCCGGGAGGGGTG‑TTTCGCCCTGCACGGTAACAAAAAATTTTTGGGT‑CCG‑GTGGTTTTTTTTTTAGCGATTTCC‑TCCCCTGCC‑CACCCGGAAATGGGGGAAAA‑GGGGGGGGGTTGGT‑TG‑ATCCCCG‑‑AACC‑TTAACCCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGt                                                                                                                     <  2:506075/239‑1 (MQ=255)                                                                                                                     tttttCCCGGGAGGGGGTTTTTCCCCTGCGCGGTACATAAAAAAT‑TTGGGG‑GCCGGTGGTTTTTTTTTTGGCGTTTTCC‑TCCCCT‑CCCCCCCGGAAAACCGGGTAAAAGGGGGGGGGTTT‑GT‑TG‑TTCCCCGC‑ACCT‑TAAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGt                                                                                                                     <  2:1298424/236‑1 (MQ=255)                                                                                                                            tggAGGGCGG‑TTTTGCCGTGCAGGTTAACT‑AAAAATTTGTGGTGGCG‑GTGGGTTTTTCTTAGGGGATTTCC‑TTCCCTCCGGCACGGAAAAGTCGGGAAAGG‑GGGGGGGGTTG‑GC‑TG‑ATCCCCCC‑ACCC‑TTAC‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTa                                                                                                             <  2:322003/238‑1 (MQ=255)                                                                                                                                    gg‑TTTTGCCCGTCGCGGTAACCAAAAATTTTTTGGT‑GGC‑GGGGGCTTTTTGTTGGGGGGGTACTTTCACGGCCGCA‑CGGAAAAGCGGGGTAAA‑GGGGGGGGGTT‑GG‑TG‑GTTTCCGG‑AACCTTTAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTAt                                                                                                       <  2:1298396/238‑1 (MQ=255)                                                                                                                                                                                gggCTTTTCTTTAGGGTTGTCC‑TTCCCTCCCGCCCCGGAAAATCGGGTAAAT‑GGGGGGGGTTT‑CT‑TA‑TTTCCCGC‑‑ACC‑TTAACCCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTCCCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGAc                                                             <  1:774417/238‑1 (MQ=255)                                                                                                                                                                                                  gTAC‑TTAACGCCCCCCCCGGAAAATCGGTAAAAA‑GGGGGGGCTTT‑GC‑TG‑ATCCCAGC‑ACCT‑TTAA‑CCGCCATGCTGGTGGGAATTACCG‑AGCCGCTGGAATTTGCCTTCCTGTTCATTTCCCCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACt                                          <  1:1318119/239‑1 (MQ=255)                                                                                                                                                                                                           ccgCCGCACCAGAAATCCGGGT‑AAA‑GGGGGGGGCTTGGT‑TG‑CTTCCCAC‑ATCC‑TTAC‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACCGGATCCCg                                  <  2:548133/237‑1 (MQ=255)                                                                                                                                                                                                            tGCCGCACCGAAAATTGGGGAAAAA‑GGGGGGGGTTT‑GT‑TG‑‑CTCCCAC‑AACC‑TTAATCCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTGCCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGa                                 <  1:1054601/239‑1 (MQ=255)                                                                                                                                                                                                                          aatcggTAAAA‑GGGGGGGGCTT‑TG‑TT‑ATTCCCCCAAACT‑TTAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCa                    <  2:1179162/235‑1 (MQ=255)                                                                                                                                                                                                                              ggTAAAA‑GGGGGGGCGTT‑TC‑TGTATCCCCGC‑ACCT‑TTAC‑CCGCCATGCTGGTGGGAATTCCCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCAcgc                 <  1:1063401/238‑1 (MQ=255)                                                                                                                                                                                                                                 aaat‑GTGGGGGGCTT‑GC‑TG‑TTCCCCGC‑ACCT‑TTAC‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGata            <  1:25485/239‑1 (MQ=255)                                                                                                                                                                                                                                 aaag‑GTGGGGGGTTT‑GC‑TG‑TTTCCCGA‑ACCC‑TTAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGata            <  1:231183/239‑1 (MQ=255)                                                                                                                                                                                                                                         ggcgtgttagC‑TT‑ATCCCCGC‑AACC‑TTAC‑CCGCCATGCTGGTGGGAATTACCG‑ACCCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATatgatg       <  1:1079359/229‑1 (MQ=255)                                                                                                                                                                                                                                             cttt‑GC‑TG‑TTCCCCCC‑AACC‑TCAC‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCTTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGAc  <  1:980106/236‑1 (MQ=255)                                                                                                                                                                                                                                                  |                                                                                                                                                                                                                                                ACCACTTCATCTACGGACAGTTTATCTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGCTT‑GC‑TG‑ATTCCCGC‑AACC‑TTAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGAC  >  NC_007779/3777506‑3777974

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑