BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080661.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,457,643 number of mapped reads = 1,304,144 (89.47%) number of supplementary alignments = 13,760 (0.94%) number of secondary alignments = 0 number of mapped bases = 85,959,230 bp number of sequenced bases = 85,927,096 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,931 duplication rate = 3.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3357 >>>>>>> ACTG content number of A's = 23,254,699 bp (27.06%) number of C's = 15,730,166 bp (18.31%) number of T's = 27,381,774 bp (31.87%) number of G's = 19,556,850 bp (22.76%) number of N's = 3,607 bp (0%) GC percentage = 41.07% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 600,855 number of insertions = 6,344 mapped reads with insertion percentage = 0.48% number of deletions = 19,939 mapped reads with deletion percentage = 1.51% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.0278X std coverageData = 0.2269X There is a 2.44% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 10737141 0.04307769006521352 0.2726478861366798 chr2 243199373 5716161 0.023504012076544293 0.35046896262762883 chr3 198022430 5537696 0.027964993662586608 0.1852387766561529 chr4 191154276 3668640 0.019192037325913652 0.15600939219879412 chr5 180915260 4049598 0.022383949258896127 0.16539271622991902 chr6 171115067 5227606 0.03055023787005267 0.22815237668102256 chr7 159138663 5425913 0.03409550449723208 0.36313035084993767 chr8 146364022 10441988 0.07134258718307153 0.3293109901734401 chr9 141213431 2839639 0.02010884502905393 0.17534781527098875 chr10 135534747 4196899 0.03096548370728873 0.204889613122853 chr11 135006516 3586278 0.026563740079034406 0.19216792108983805 chr12 133851895 2724104 0.020351628193235514 0.1591892186627059 chr13 115169878 1868764 0.016226152466706615 0.1417110405047797 chr14 107349540 1661138 0.015474104500121752 0.13977777126777127 chr15 102531392 1575318 0.015364250589712075 0.1457077929553997 chr16 90354753 2148931 0.0237832646169704 0.17348464862034862 chr17 81195210 1428200 0.017589707570187945 0.14943899990908208 chr18 78077248 2777058 0.035568082522580716 0.2532471844640945 chr19 59128983 1381465 0.023363584656952412 0.20119531210599034 chr20 63025520 2254247 0.035767209854040076 0.21076028402994365 chr21 48129895 1280298 0.026600889114759132 0.18253665312740047 chr22 51304566 849877 0.016565328707780123 0.14147588183856286 chrMT 16571 10694 0.6453442761450727 0.9481993616869958 chrX 155270560 4418985 0.028459902508241097 0.19198532377638575 chrY 59373566 152592 0.002570032596660945 0.05872087547722636