BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238074.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,606,572 number of mapped reads = 1,283,901 (79.92%) number of supplementary alignments = 14,627 (0.91%) number of secondary alignments = 0 number of mapped bases = 84,424,504 bp number of sequenced bases = 84,385,760 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 175,138 duplication rate = 10.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1445 >>>>>>> ACTG content number of A's = 22,723,380 bp (26.93%) number of C's = 15,946,987 bp (18.9%) number of T's = 26,448,741 bp (31.34%) number of G's = 19,255,099 bp (22.82%) number of N's = 11,553 bp (0.01%) GC percentage = 41.72% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 660,746 number of insertions = 5,712 mapped reads with insertion percentage = 0.44% number of deletions = 22,234 mapped reads with deletion percentage = 1.71% homopolymer indels = 45.99% >>>>>>> Coverage mean coverageData = 0.0273X std coverageData = 0.3497X There is a 1.33% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.33% of reference with a coverageData >= 3X There is a 0.18% of reference with a coverageData >= 4X There is a 0.1% of reference with a coverageData >= 5X There is a 0.06% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% 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% 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 4878500 0.01957266938965821 0.39144025243255864 chr2 243199373 8212166 0.03376721699031683 0.39155384255551084 chr3 198022430 3582735 0.018092571634435554 0.24174733756025896 chr4 191154276 3613534 0.018903757088855288 0.2484420422548688 chr5 180915260 3298583 0.018232751620841713 0.24587078620523015 chr6 171115067 3023566 0.017669782404374713 0.25136680124250305 chr7 159138663 3430520 0.02155679792282784 0.3043691394782308 chr8 146364022 9195200 0.06282418229802403 0.5672813562745705 chr9 141213431 2593643 0.01836682942715272 0.25446048675098665 chr10 135534747 4992599 0.03683630294451356 0.39157585480158785 chr11 135006516 7790521 0.05770477774569044 0.628740761244246 chr12 133851895 2738047 0.02045579556419429 0.26231607527335626 chr13 115169878 1821760 0.015818024917939048 0.23058169932877084 chr14 107349540 7446724 0.06936894186970899 0.5028687518427175 chr15 102531392 1670878 0.016296257832918135 0.2331610545817401 chr16 90354753 4110488 0.04549277003723313 0.4011653312393127 chr17 81195210 2904933 0.03577714744502785 0.3954749669022063 chr18 78077248 1254364 0.016065678954258224 0.2979213358195849 chr19 59128983 1138750 0.019258744903493434 0.2988975696743841 chr20 63025520 1041346 0.01652260861949255 0.23542657467922898 chr21 48129895 1143371 0.023755942122873942 0.28972706538733484 chr22 51304566 657814 0.012821743780076026 0.19366910297927065 chrMT 16571 87366 5.272222557479934 4.835512169870127 chrX 155270560 3570881 0.022997798165988452 0.29548595660283306 chrY 59373566 226215 0.003810028860318075 0.10988852586883509