BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156427.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 = 3,198,590 number of mapped reads = 3,131,273 (97.9%) number of supplementary alignments = 391,885 (12.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,568,020 number of mapped paired reads (second in pair) = 1,563,253 number of mapped paired reads (both in pair) = 3,088,164 number of mapped paired reads (singletons) = 43,109 number of mapped bases = 355,979,153 bp number of sequenced bases = 355,739,538 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,567,254 duplication rate = 67% >>>>>>> Insert size mean insert size = 922,605.1237 std insert size = 9,198,944.7645 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 52.561 >>>>>>> ACTG content number of A's = 106,532,011 bp (29.95%) number of C's = 70,430,672 bp (19.8%) number of T's = 105,654,317 bp (29.7%) number of G's = 73,119,712 bp (20.55%) number of N's = 2,826 bp (0%) GC percentage = 40.35% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 3,105,877 number of insertions = 41,092 mapped reads with insertion percentage = 1.26% number of deletions = 103,263 mapped reads with deletion percentage = 3.21% homopolymer indels = 40.91% >>>>>>> Coverage mean coverageData = 0.115X std coverageData = 2.2486X There is a 2.28% of reference with a coverageData >= 1X There is a 1.77% of reference with a coverageData >= 2X There is a 1.36% of reference with a coverageData >= 3X There is a 1.11% of reference with a coverageData >= 4X There is a 0.85% of reference with a coverageData >= 5X There is a 0.71% of reference with a coverageData >= 6X There is a 0.54% of reference with a coverageData >= 7X There is a 0.46% of reference with a coverageData >= 8X There is a 0.35% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.24% of reference with a coverageData >= 11X There is a 0.22% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% 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 0.02% of reference with a coverageData >= 27X There is a 0.02% 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 0.01% 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 31653252 0.12699367356842012 1.5955987228983621 chr2 243199373 26997236 0.11100865790472247 6.744402741579817 chr3 198022430 23061945 0.11646127663416715 1.0749356554229317 chr4 191154276 30663678 0.1604132465234521 1.5001930540831414 chr5 180915260 28445265 0.1572297715516093 1.242092555954453 chr6 171115067 21672294 0.12665333555928188 1.2632046084369315 chr7 159138663 22870432 0.14371386292217372 1.5054763397695547 chr8 146364022 16350721 0.11171270628242233 1.5595433980274314 chr9 141213431 15170715 0.10743110547324639 1.3235147233101892 chr10 135534747 14973985 0.11048078320461985 1.5276729504626798 chr11 135006516 14358374 0.1063531926118292 1.0637369076728584 chr12 133851895 15032459 0.11230665804171096 1.0649072842293479 chr13 115169878 11149392 0.09680822966574645 0.9742278509662651 chr14 107349540 8262538 0.07696854592949351 0.8793666623262855 chr15 102531392 10651080 0.10388116061079128 1.0109500123423345 chr16 90354753 9994027 0.11060875790341655 1.208427994050406 chr17 81195210 8329446 0.10258543576646947 1.0521499149133169 chr18 78077248 9370486 0.12001557739330157 1.4805485056959464 chr19 59128983 7816967 0.1322019524672021 1.2752271094013625 chr20 63025520 6894549 0.10939297287828803 1.0657842555213382 chr21 48129895 4428559 0.09201264619422087 1.0687941952022377 chr22 51304566 4828249 0.09410953793079548 0.9580066951255845 chrMT 16571 675721 40.77732182728864 36.71852677479229 chrX 155270560 9689793 0.062405861098201745 0.7793516139082678 chrY 59373566 2637990 0.04443037832694772 0.9484115554879565