BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818904.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,713,973 number of mapped reads = 1,684,011 (98.25%) number of supplementary alignments = 22,233 (1.3%) number of secondary alignments = 0 number of mapped bases = 156,106,684 bp number of sequenced bases = 156,007,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 355,985 duplication rate = 17.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2602 >>>>>>> ACTG content number of A's = 43,351,590 bp (27.79%) number of C's = 32,006,860 bp (20.52%) number of T's = 45,438,414 bp (29.13%) number of G's = 35,207,863 bp (22.57%) number of N's = 2,412 bp (0%) GC percentage = 43.08% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 974,470 number of insertions = 23,731 mapped reads with insertion percentage = 1.36% number of deletions = 50,021 mapped reads with deletion percentage = 2.9% homopolymer indels = 39.14% >>>>>>> Coverage mean coverageData = 0.0504X std coverageData = 0.6599X There is a 3.55% of reference with a coverageData >= 1X There is a 0.88% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 14822071 0.05946653589280325 0.9774854883035509 chr2 243199373 11748295 0.04830725858820368 0.9286426457353781 chr3 198022430 9675086 0.04885853587394115 0.2951494563646654 chr4 191154276 7750147 0.04054393740059469 0.36826150033509447 chr5 180915260 6901236 0.03814623487261384 0.28031746156662274 chr6 171115067 7697443 0.04498401651562337 0.3110405389402614 chr7 159138663 14012968 0.08805508187535797 1.5265630618021262 chr8 146364022 13535487 0.09247823894863999 0.5199390922185997 chr9 141213431 5742591 0.04066603976218098 0.5605456993278326 chr10 135534747 7272351 0.0536567275991595 0.8957374853363105 chr11 135006516 6949358 0.05147424143587262 0.3879790468442948 chr12 133851895 6051136 0.04520769765717549 0.2891495766919296 chr13 115169878 4678747 0.04062474564746869 0.26727887088556657 chr14 107349540 4560032 0.04247835621838715 0.3072812584831646 chr15 102531392 4331174 0.0422424187901399 0.27971243455069816 chr16 90354753 4009457 0.044374610818757924 0.6663088617449464 chr17 81195210 3971618 0.04891443719401674 0.4169338566419468 chr18 78077248 2996264 0.03837563537075487 0.6253205506691459 chr19 59128983 2808757 0.04750220378388717 0.866342275992085 chr20 63025520 6499120 0.1031188635968414 0.4707373916137024 chr21 48129895 1504378 0.03125662335228448 0.29262631687609114 chr22 51304566 1469310 0.028638971431899453 0.24649748201756846 chrMT 16571 127105 7.670327680888299 5.194492551770939 chrX 155270560 6392365 0.041169201682534025 0.33104088967238504 chrY 59373566 600188 0.010108673614113054 0.7685561861449602