Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	ACB143	5,386,507	+C	intergenic (‑516/+1135)	CJ019_05070 ← / ← nptII	hypothetical protein/neomycin phosphotransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	ACB143	5,386,507	1	.	C	92.6%	87.9 / 0.6	27	intergenic (‑516/+1135)	CJ019_05070/nptII	hypothetical protein/neomycin phosphotransferase
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base C (11/14);  total (12/15)
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

CCTTTTTTATTGATAACAAAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCCGT‑CGT‑‑‑CA‑GGAT‑C‑‑A‑‑T‑CCGGGCGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCTTGG  >  ACB143/5386410‑5386604                                                                                                       |                                                                                                        ccTTTTTTATTGATAACAAAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGc                                                                 >  1:140318/1‑136 (MQ=255) ccTTTTTTATTGATAACAAAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGc                                                                 >  8:196722/1‑136 (MQ=255)          ttGATAACAAAAATTGATCTAATTCTTTAATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGGCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGaa                                                         <  1:381239/135‑1 (MQ=255)                aCAAAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCAc                                                   >  4:93987/1‑135 (MQ=255)                       ttGATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCgg                                            <  4:38452/135‑1 (MQ=255)                                     tCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGGCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTAtt                               <  8:284278/134‑1 (MQ=255)                                     tCATTAAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGGT‑‑‑TA‑CGCTAC‑‑AACC‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTAtt                               <  6:40934/134‑1 (MQ=255)                                       aTTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCGCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTgcgc                           <  7:90429/136‑1 (MQ=255)                                       aTTTAACACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑C‑‑AACC‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTgcgc                           <  7:36010/136‑1 (MQ=255)                                              aCCCTAATATGACATCTCGGCCGGCTTGGCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGt                    <  1:155497/136‑1 (MQ=255)                                                ccTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGCGGGCTTTTTTATTGCGCTGCGGGTGc                  >  6:291024/1‑136 (MQ=255)                                                    ttatGACATCGCGGCCGGCTGGTCGACGACGGGGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAgg              <  2:383321/135‑1 (MQ=255)                                                    atatGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAgg              <  6:139809/136‑1 (MQ=255)                                                    atatGACATCTCGGCCGGCGTGTCGACGACGGCGGTCGCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGAGGTTGCCAgg              <  8:255959/136‑1 (MQ=255)                                                    atatCACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAgg              <  1:143764/136‑1 (MQ=255)                                                     tatGACATCTCGGCCGGCTTGGCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAgg              <  4:337739/135‑1 (MQ=255)                                                             ctcGGCCGGCTTGTTGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCGTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCt     >  5:3657/1‑136 (MQ=255)                                                             ctcGGCCGGCTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCt     >  5:69561/1‑136 (MQ=255)                                                             ctcGGCCGGCTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCt     >  6:362927/1‑136 (MQ=255)                                                             ctcGGCCGGCTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCt     >  1:216374/1‑136 (MQ=255)                                                             ctcGGCCGGCTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTATTATTGCGCTGCGGGAGCCAGGGCGTGccc      >  3:212377/1‑135 (MQ=255)                                                              tcGGCCGGCTTGTCGACCACGGCGGTCTCAGT‑GGTGTACG‑GTAC‑A‑‑A‑‑TCCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGATGCGGGTGCCAGGGCGTGACCtt    >  5:313863/1‑136 (MQ=255)                                                                ggccggcTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCTTgg  >  5:132480/1‑136 (MQ=255)                                                                ggccggcTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCTTgg  >  7:312245/1‑136 (MQ=255)                                                                 gccggcTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCtt    <  4:348427/133‑1 (MQ=255)                                                                 gccggcTTGTCGACGACGGCGGTCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCtt    <  4:192186/133‑1 (MQ=255)                                                                 gccggcTTGTCGACGACGGCGGGCTCAGT‑GGTG‑‑TACGGTA‑CAAA‑‑C‑CCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCtt    <  4:183160/133‑1 (MQ=255)                                                                                                       |                                                                                                        CCTTTTTTATTGATAACAAAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCCGT‑CGT‑‑‑CA‑GGAT‑C‑‑A‑‑T‑CCGGGCGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCTTGG  >  ACB143/5386410‑5386604

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑