BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237840.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 = 1,218,677 number of mapped reads = 756,195 (62.05%) number of supplementary alignments = 6,241 (0.51%) number of secondary alignments = 0 number of mapped bases = 47,906,686 bp number of sequenced bases = 47,887,698 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,573 duplication rate = 6.53% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7072 >>>>>>> ACTG content number of A's = 12,874,660 bp (26.89%) number of C's = 8,639,748 bp (18.04%) number of T's = 15,400,627 bp (32.16%) number of G's = 10,937,869 bp (22.84%) number of N's = 34,794 bp (0.07%) GC percentage = 40.88% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 366,258 number of insertions = 3,846 mapped reads with insertion percentage = 0.5% number of deletions = 11,695 mapped reads with deletion percentage = 1.53% homopolymer indels = 47.9% >>>>>>> Coverage mean coverageData = 0.0155X std coverageData = 0.188X There is a 1.13% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 3718866 0.014920187500756518 0.24117843565338806 chr2 243199373 4488572 0.01845634692487468 0.21144957517640647 chr3 198022430 3226393 0.01629306841654251 0.16798041211862436 chr4 191154276 3128703 0.016367423556876124 0.17724641423254195 chr5 180915260 3017296 0.01667795187647521 0.17058034040486142 chr6 171115067 2809974 0.01642154632706891 0.18362845412258313 chr7 159138663 2593283 0.01629574454826229 0.19372070698371247 chr8 146364022 2643137 0.01805865241937667 0.2137546116415213 chr9 141213431 1870175 0.013243605702066683 0.17469354536149634 chr10 135534747 2379248 0.01755452422838846 0.21839891542194456 chr11 135006516 2132175 0.01579312660731131 0.1770288124281478 chr12 133851895 2263716 0.016912095267683735 0.17516361949430345 chr13 115169878 1465534 0.012724976577642984 0.14698366001732638 chr14 107349540 1378927 0.012845206416347942 0.15249429918077836 chr15 102531392 1232558 0.012021274421008544 0.14280384660090403 chr16 90354753 1287232 0.014246422653604067 0.16620488075821688 chr17 81195210 1184880 0.014592979068592839 0.16497138463374267 chr18 78077248 1234192 0.01580731943830807 0.2687531855442874 chr19 59128983 835213 0.01412527254189371 0.1905961665533308 chr20 63025520 973749 0.015450074826832052 0.16540092269768353 chr21 48129895 612479 0.012725541994222093 0.15861525088452905 chr22 51304566 487566 0.009503364671284813 0.12488950649904561 chrMT 16571 97226 5.867237945808943 4.782553747259922 chrX 155270560 2708451 0.01744342906987648 0.18019622409656888 chrY 59373566 137141 0.0023097989431862657 0.07772389474338842