BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084352.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 = 3,140,716 number of mapped reads = 1,634,324 (52.04%) number of supplementary alignments = 8,290 (0.26%) number of secondary alignments = 0 number of mapped bases = 104,213,077 bp number of sequenced bases = 104,179,072 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 54,190 duplication rate = 2.75% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5875 >>>>>>> ACTG content number of A's = 29,268,523 bp (28.09%) number of C's = 19,534,745 bp (18.75%) number of T's = 31,826,224 bp (30.55%) number of G's = 23,548,415 bp (22.6%) number of N's = 1,165 bp (0%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 863,531 number of insertions = 7,482 mapped reads with insertion percentage = 0.45% number of deletions = 21,310 mapped reads with deletion percentage = 1.29% homopolymer indels = 46.36% >>>>>>> Coverage mean coverageData = 0.0337X std coverageData = 0.2577X There is a 2.99% of reference with a coverageData >= 1X There is a 0.29% 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 7375289 0.029589852054972412 0.3405083985845706 chr2 243199373 8621896 0.035451966399600875 0.3321093059470711 chr3 198022430 7200105 0.03636004769762698 0.2099764664889352 chr4 191154276 7199529 0.03766344729845332 0.2179085690791515 chr5 180915260 7557592 0.041774209649313165 0.2240374941572793 chr6 171115067 5869635 0.03430226865995383 0.2266608070364785 chr7 159138663 5519006 0.034680484905167265 0.2718739843659392 chr8 146364022 5664339 0.038700350828019744 0.27200245684929203 chr9 141213431 4082945 0.028913290832796208 0.24843224161479086 chr10 135534747 5126891 0.037827133731249005 0.2728982573021968 chr11 135006516 4421857 0.032752915422245246 0.23569506837576457 chr12 133851895 4830476 0.03608821526209995 0.21002451561344904 chr13 115169878 3259065 0.028297894003152455 0.18521738650924277 chr14 107349540 3128423 0.029142397815584493 0.19800493274345438 chr15 102531392 2989626 0.029158152851372583 0.192492857953615 chr16 90354753 3278112 0.036280459977573065 0.22739570539420415 chr17 81195210 2791931 0.03438541510022574 0.22413658551684731 chr18 78077248 3131243 0.04010442325016374 0.4872850615093642 chr19 59128983 1794887 0.030355451910952028 0.31004265824339583 chr20 63025520 2040200 0.0323710141542664 0.2032578542407433 chr21 48129895 1319264 0.027410489883678325 0.1884243468035269 chr22 51304566 1269967 0.0247534888025366 0.17273990201683695 chrMT 16571 40471 2.4422786796210247 2.033351124027733 chrX 155270560 5462556 0.03518088683392396 0.2258850415262789 chrY 59373566 237772 0.0040046777719229465 0.08816817504312788