BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094146.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 369,324 number of mapped reads = 337,492 (91.38%) number of supplementary alignments = 21,860 (5.92%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 169,658 number of mapped paired reads (second in pair) = 167,834 number of mapped paired reads (both in pair) = 334,196 number of mapped paired reads (singletons) = 3,296 number of mapped bases = 43,000,664 bp number of sequenced bases = 42,029,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 308,257 duplication rate = 47.53% >>>>>>> Insert size mean insert size = 1,468,881.6998 std insert size = 10,881,881.1234 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 46.0908 >>>>>>> ACTG content number of A's = 11,567,008 bp (27.52%) number of C's = 9,429,665 bp (22.44%) number of T's = 10,975,731 bp (26.11%) number of G's = 10,056,922 bp (23.93%) number of N's = 422 bp (0%) GC percentage = 46.36% >>>>>>> Mismatches and indels general error rate = 0.0394 number of mismatches = 1,604,904 number of insertions = 26,626 mapped reads with insertion percentage = 7.74% number of deletions = 127,848 mapped reads with deletion percentage = 36.67% homopolymer indels = 29.33% >>>>>>> Coverage mean coverageData = 0.0139X std coverageData = 2.3365X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 721836 0.0028960248809169467 0.8135425865866205 chr2 243199373 1987702 0.008173137847686803 2.181584548006855 chr3 198022430 626822 0.0031654090902732586 0.8089896763167085 chr4 191154276 832675 0.004356036482280941 1.0434544748479786 chr5 180915260 912683 0.005044809376500357 1.5005963545204137 chr6 171115067 578419 0.0033802926308061465 1.0186853801158469 chr7 159138663 930030 0.005844148634075177 1.4132576343116994 chr8 146364022 830278 0.005672691885988211 1.596411361119057 chr9 141213431 640546 0.004536013291823495 1.5105537907350897 chr10 135534747 568932 0.00419768371279728 0.8821361797349077 chr11 135006516 828881 0.006139562923022175 1.4157314849923779 chr12 133851895 934636 0.006982613133717681 1.5559916155500768 chr13 115169878 791237 0.006870173119398459 1.4176272530439045 chr14 107349540 176371 0.0016429599977792174 0.4492001113298957 chr15 102531392 476519 0.004647542481428517 1.0240369693525744 chr16 90354753 205642 0.002275940038262293 0.5563691580538361 chr17 81195210 570042 0.0070206358232215915 1.3717066833158245 chr18 78077248 201730 0.00258372323778625 0.5950959138303294 chr19 59128983 147064 0.0024871728302852765 0.5594346840799187 chr20 63025520 285541 0.004530561588385149 1.3995576005510952 chr21 48129895 261272 0.005428476417827215 1.5975163176070184 chr22 51304566 139967 0.00272815873737242 0.6432531619178032 chrMT 16571 2026278 122.27855892824815 486.7613460467504 chrX 155270560 27320035 0.1759511590606745 7.137121560666994 chrY 59373566 5526 9.307172151324042E-5 0.03999974375674186