Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_007779	3,777,754	A→C	38.6%	T315P (ACC→CCC)	Y75_RS18735 →	PTS transporter subunit EIIC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_007779	3,777,754	0	A	C	38.6%	11.7 / 8.9	32	T315P (ACC→CCC)	Y75_RS18735	PTS transporter subunit EIIC
Reads supporting (aligned to +/- strand):  ref base A (8/10);  new base C (4/8);  total (12/20)
Fisher's exact test for biased strand distribution p-value = 7.09e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01

CTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGCTT‑GC‑TG‑ATTCCCGC‑AACC‑TTAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGCCA  >  NC_007779/3777531‑3777985                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                           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)                            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)                                                                        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)                                                                                                                                                                                                                            tG‑ATCCCCGC‑ATCC‑TTAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAAt       <  1:203341/238‑1 (MQ=255)                                                                                                                                                                                                                            tG‑ATCCCCCC‑ACCT‑TAAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAAt       <  1:398282/238‑1 (MQ=255)                                                                                                                                                                                                                             ttctacccAC‑AACT‑TAAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGTAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAAt       <  2:1681438/233‑1 (MQ=255)                                                                                                                                                                                                                             taatccccGC‑AACT‑TTAA‑CCGCCATGCTGGTGGGAATTGCCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAAt       <  1:591184/233‑1 (MQ=255)                                                                                                                                                                                                                                 tCCCGC‑AACC‑TTAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGCCa  >  2:330797/1‑239 (MQ=255)                                                                                                                                                                                                                                 tCCCGC‑AACC‑TTAA‑CCGCCATGCTGGTGGCAATTACCG‑CACCGCTGGAATTTACCTTCCTGCTCATTTCACCGTTGCTGTTTGCGGGACACGCCGTGCTGGCGGCCTCAATGTCGACCGTGATGTCTCTCTTTGGAGGGGTGGGCAACCTGGGCGGAGGGCGGATTGATGAGGATTTACCGCAAAACTGCATCACGATGTTCCGCAACGACGCGGATATGAAGCTGACCCAGATCGcc   >  2:322272/1‑238 (MQ=255)                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                           CTTTGGTCCGGCAGCTGTTGAAGGCGGCATTCAGATGTACTGGGCGCAGCATCTGCAAGAGTTCAGTTTGAGCGCCGAGCCGCTGAAATCGTTGTTCCCGGAAGGCGG‑TTTTGCCCTGCACGGTAACTCAAAAATCTTTGGT‑GCC‑GTGGGCATTTCTTTAGCGATGTAC‑TTCACTGCCGCACCGGAAAATCGGGTAAAA‑GTGGCGGGCTT‑GC‑TG‑ATTCCCGC‑AACC‑TTAA‑CCGCCATGCTGGTGGGAATTACCG‑AACCGCTGGAATTTACCTTCCTGTTCATTTCACCGTTGCTGTTTGCGGTACACGCCGTGCTGGCGGCCTCAATGTCGACCGTAATGTATCTCTTTGGTGTGGTGGGCAACATGGGCGGAGGTCTGATTGACTAGGTTTTACCGCAAAACTGGATCCCGATGTTCAGCAACCACGCGGATATGATGCTGACCCAAATCGCCA  >  NC_007779/3777531‑3777985

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑