BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21671996.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 286,922,860 number of mapped reads = 283,503,164 (98.81%) number of supplementary alignments = 3,933,451 (1.37%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 141,794,327 number of mapped paired reads (second in pair) = 141,708,837 number of mapped paired reads (both in pair) = 282,639,654 number of mapped paired reads (singletons) = 863,510 number of mapped bases = 38,954,098,520 bp number of sequenced bases = 38,934,991,205 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 143,185,864 duplication rate = 39.67% >>>>>>> Insert size mean insert size = 136,853.7223 std insert size = 3,669,140.4731 median insert size = 287 >>>>>>> Mapping quality mean mapping quality = 54.0832 >>>>>>> ACTG content number of A's = 10,811,352,118 bp (27.77%) number of C's = 7,680,091,042 bp (19.73%) number of T's = 11,716,165,398 bp (30.09%) number of G's = 8,726,724,561 bp (22.41%) number of N's = 658,086 bp (0%) GC percentage = 42.14% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 402,646,539 number of insertions = 5,654,809 mapped reads with insertion percentage = 1.91% number of deletions = 9,860,265 mapped reads with deletion percentage = 3.37% homopolymer indels = 46.53% >>>>>>> Coverage mean coverageData = 12.5833X std coverageData = 264.4274X There is a 57.58% of reference with a coverageData >= 1X There is a 51.77% of reference with a coverageData >= 2X There is a 47.11% of reference with a coverageData >= 3X There is a 43.6% of reference with a coverageData >= 4X There is a 40.55% of reference with a coverageData >= 5X There is a 37.98% of reference with a coverageData >= 6X There is a 35.69% of reference with a coverageData >= 7X There is a 33.66% of reference with a coverageData >= 8X There is a 31.82% of reference with a coverageData >= 9X There is a 30.14% of reference with a coverageData >= 10X There is a 28.61% of reference with a coverageData >= 11X There is a 27.2% of reference with a coverageData >= 12X There is a 25.89% of reference with a coverageData >= 13X There is a 24.68% of reference with a coverageData >= 14X There is a 23.55% of reference with a coverageData >= 15X There is a 22.49% of reference with a coverageData >= 16X There is a 21.5% of reference with a coverageData >= 17X There is a 20.57% of reference with a coverageData >= 18X There is a 19.69% of reference with a coverageData >= 19X There is a 18.87% of reference with a coverageData >= 20X There is a 18.09% of reference with a coverageData >= 21X There is a 17.35% of reference with a coverageData >= 22X There is a 16.65% of reference with a coverageData >= 23X There is a 15.99% of reference with a coverageData >= 24X There is a 15.36% of reference with a coverageData >= 25X There is a 14.77% of reference with a coverageData >= 26X There is a 14.2% of reference with a coverageData >= 27X There is a 13.66% of reference with a coverageData >= 28X There is a 13.14% of reference with a coverageData >= 29X There is a 12.65% of reference with a coverageData >= 30X There is a 12.18% of reference with a coverageData >= 31X There is a 11.74% of reference with a coverageData >= 32X There is a 11.31% of reference with a coverageData >= 33X There is a 10.9% of reference with a coverageData >= 34X There is a 10.51% of reference with a coverageData >= 35X There is a 10.13% of reference with a coverageData >= 36X There is a 9.77% of reference with a coverageData >= 37X There is a 9.43% of reference with a coverageData >= 38X There is a 9.1% of reference with a coverageData >= 39X There is a 8.78% of reference with a coverageData >= 40X There is a 8.48% of reference with a coverageData >= 41X There is a 8.19% of reference with a coverageData >= 42X There is a 7.91% of reference with a coverageData >= 43X There is a 7.64% of reference with a coverageData >= 44X There is a 7.38% of reference with a coverageData >= 45X There is a 7.13% of reference with a coverageData >= 46X There is a 6.89% of reference with a coverageData >= 47X There is a 6.66% of reference with a coverageData >= 48X There is a 6.44% of reference with a coverageData >= 49X There is a 6.23% of reference with a coverageData >= 50X There is a 6.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3236250627 12.983922022003709 95.22811479953143 chr2 243199373 4460319925 18.340178553832043 473.3288020257589 chr3 198022430 2217172379 11.196571918645782 22.54833918811368 chr4 191154276 2246753782 11.753615085230948 65.06642190472485 chr5 180915260 2268799323 12.540674142137043 27.912005739834925 chr6 171115067 2359553218 13.789277936582872 268.5997080882494 chr7 159138663 2117259203 13.304492843451877 576.3098856489364 chr8 146364022 1728438888 11.809178679170213 64.92500119757243 chr9 141213431 1855290153 13.138198964941232 694.2300934519168 chr10 135534747 1985675708 14.650676316974273 142.45394432316414 chr11 135006516 1707220327 12.645466141797186 164.18287285347898 chr12 133851895 1840953274 13.753658653842741 28.859132004650114 chr13 115169878 1265117774 10.984797379050796 23.40443519298187 chr14 107349540 1251586101 11.658979637919268 28.872170064506804 chr15 102531392 1025400152 10.000841030228088 21.797091995182278 chr16 90354753 1113685875 12.32570327539936 78.7851053020459 chr17 81195210 1111036650 13.683524557667873 139.69461156618152 chr18 78077248 1118585628 14.326652855387525 428.57064817985105 chr19 59128983 725769343 12.274341721723845 103.15697841107709 chr20 63025520 881913022 13.992951141061589 32.560233815767155 chr21 48129895 479343374 9.95936878732023 53.18518824369437 chr22 51304566 424959798 8.283079482633184 33.799034161222956 chrMT 16571 1874276 113.10578721863496 330.69994959842575 chrX 155270560 1265430237 8.149840104911066 57.81358846507495 chrY 59373566 265709483 4.475215165617642 52.42981661283963