BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173840.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,932,788 number of mapped reads = 4,809,671 (97.5%) number of supplementary alignments = 446,119 (9.04%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,406,758 number of mapped paired reads (second in pair) = 2,402,913 number of mapped paired reads (both in pair) = 4,726,872 number of mapped paired reads (singletons) = 82,799 number of mapped bases = 569,044,431 bp number of sequenced bases = 568,760,409 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,693,051 duplication rate = 64.74% >>>>>>> Insert size mean insert size = 810,219.3326 std insert size = 8,143,607.9778 median insert size = 198 >>>>>>> Mapping quality mean mapping quality = 52.8659 >>>>>>> ACTG content number of A's = 172,208,327 bp (30.28%) number of C's = 110,498,440 bp (19.43%) number of T's = 172,012,586 bp (30.24%) number of G's = 114,034,387 bp (20.05%) number of N's = 6,669 bp (0%) GC percentage = 39.48% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 5,596,442 number of insertions = 58,240 mapped reads with insertion percentage = 1.17% number of deletions = 117,502 mapped reads with deletion percentage = 2.38% homopolymer indels = 43.74% >>>>>>> Coverage mean coverageData = 0.1838X std coverageData = 2.7123X There is a 3.87% of reference with a coverageData >= 1X There is a 3.04% of reference with a coverageData >= 2X There is a 2.32% of reference with a coverageData >= 3X There is a 1.91% of reference with a coverageData >= 4X There is a 1.45% of reference with a coverageData >= 5X There is a 1.18% of reference with a coverageData >= 6X There is a 0.88% of reference with a coverageData >= 7X There is a 0.72% of reference with a coverageData >= 8X There is a 0.53% of reference with a coverageData >= 9X There is a 0.44% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.18% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.09% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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% 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 43332968 0.1738529991465899 1.927217417818544 chr2 243199373 48802103 0.2006670592855517 8.144854413186057 chr3 198022430 48420576 0.24452066364401245 1.4515195856050804 chr4 191154276 28113002 0.147069699869021 1.2765465111339387 chr5 180915260 37871786 0.2093343922452976 1.3197268649652234 chr6 171115067 30469867 0.17806653460855087 1.4080828720582637 chr7 159138663 31754092 0.1995372551295093 1.8072660496291137 chr8 146364022 33334959 0.22775377817917575 1.7908336231657829 chr9 141213431 23638120 0.16739285939451468 1.4220699906904077 chr10 135534747 29559346 0.21809422789567018 2.2509614112275824 chr11 135006516 20128256 0.14909099646716312 1.1225208262579425 chr12 133851895 25423897 0.18994050850008512 1.256203405524395 chr13 115169878 15322759 0.13304484875811018 1.0571725807613304 chr14 107349540 16835573 0.15682948431823743 1.142728022205519 chr15 102531392 18098202 0.1765137646819425 1.2016588988743293 chr16 90354753 17876840 0.1978516835744103 1.5528458197491786 chr17 81195210 22183932 0.27321725013088827 1.6461157883661497 chr18 78077248 10492598 0.13438739541639583 1.9244432575625066 chr19 59128983 8410477 0.14223950038173327 1.3264257643691795 chr20 63025520 24131131 0.3828787291243293 1.9387150877839208 chr21 48129895 7273624 0.15112486740309738 1.1695618419706983 chr22 51304566 3899417 0.07600526237762152 0.7649762176548915 chrMT 16571 1443266 87.0958904109589 66.72472591701812 chrX 155270560 21253284 0.1368790323162356 1.0630875801816853 chrY 59373566 974356 0.016410602657755135 0.6545393138554516