BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504735.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 2,158,225 number of mapped reads = 1,899,900 (88.03%) number of secondary alignments = 0 number of mapped bases = 60,790,048 bp number of sequenced bases = 60,790,048 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 408,402 duplication rate = 8.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 7.6028 >>>>>>> ACTG content number of A's = 17,754,611 bp (29.21%) number of C's = 11,956,850 bp (19.67%) number of T's = 18,962,864 bp (31.19%) number of G's = 12,115,622 bp (19.93%) number of N's = 101 bp (0%) GC percentage = 39.6% >>>>>>> Mismatches and indels general error rate = 0.0005 number of mismatches = 30,606 >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 1.6493X There is a 0.94% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.11% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% 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% 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 4907278 0.019688127477122716 0.4092368457520063 chr2 243199373 11546356 0.0474769151645798 5.7038249095448394 chr3 198022430 3233318 0.016328039202427726 0.31919911542791957 chr4 191154276 3172184 0.016594889041352128 0.3164899671223768 chr5 180915260 3284744 0.018156257244413766 0.36599758946818073 chr6 171115067 3189514 0.01863958595767607 0.45632375536585884 chr7 159138663 2587672 0.016260485988876253 0.2543086751285451 chr8 146364022 3010662 0.020569686176019404 0.541857442925644 chr9 141213431 2672392 0.018924488846956775 0.8267587736425043 chr10 135534747 2039644 0.01504886418535905 0.2820397982180307 chr11 135006516 2907952 0.021539345552773172 0.454831141993736 chr12 133851895 3036862 0.022688225669124817 0.7101915182287136 chr13 115169878 1750632 0.015200432877075723 0.43219640754325844 chr14 107349540 1812042 0.01687983013248124 0.37702878841741616 chr15 102531392 1179808 0.011506797840021522 0.1939636667269885 chr16 90354753 1083130 0.011987526544397725 0.22238200571455408 chr17 81195210 962080 0.011848974834845554 0.1931905155241944 chr18 78077248 1185140 0.015179069836067993 0.3686798825802494 chr19 59128983 450608 0.007620763577144562 0.12212014485265457 chr20 63025520 1010976 0.016040740322332922 0.3130490160036667 chr21 48129895 491352 0.010208873300056025 0.19435369814097578 chr22 51304566 323994 0.006315110432860888 0.15954441212153364 chrMT 16571 0 0.0 0.0 chrX 155270560 4659400 0.030008264283969865 0.5148694703881815 chrY 59373566 292308 0.0049232010083409845 0.1627390232114098