BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717084.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,856,124 number of mapped reads = 1,718,100 (92.56%) number of supplementary alignments = 27,789 (1.5%) number of secondary alignments = 0 number of mapped bases = 134,940,364 bp number of sequenced bases = 134,881,636 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,448 duplication rate = 2.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.08 >>>>>>> ACTG content number of A's = 32,723,151 bp (24.26%) number of C's = 27,181,005 bp (20.15%) number of T's = 42,493,118 bp (31.5%) number of G's = 32,476,848 bp (24.08%) number of N's = 7,514 bp (0.01%) GC percentage = 44.23% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,109,462 number of insertions = 12,547 mapped reads with insertion percentage = 0.72% number of deletions = 33,794 mapped reads with deletion percentage = 1.94% homopolymer indels = 43.38% >>>>>>> Coverage mean coverageData = 0.0436X std coverageData = 0.4763X There is a 3.72% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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 10565991 0.042391031796065216 0.7733428234439728 chr2 243199373 11459266 0.04711881391240264 0.7110864113746406 chr3 198022430 9055875 0.04573156182357726 0.24470168231782277 chr4 191154276 8637776 0.04518745895069593 0.269514631540123 chr5 180915260 8414765 0.0465121902928476 0.25261023556842294 chr6 171115067 7448868 0.043531339060867154 0.29705992756529537 chr7 159138663 7369343 0.046307684512845254 0.5689671983342168 chr8 146364022 6762292 0.04620187329916364 0.6404498124681083 chr9 141213431 5660749 0.04008647732665033 0.5243187341126699 chr10 135534747 6525100 0.04814337389068207 0.4470605140841496 chr11 135006516 6086314 0.04508163146732858 0.454079713117595 chr12 133851895 5982943 0.044698231579015 0.24731563308034 chr13 115169878 4405847 0.038255202458406704 0.22016958499464911 chr14 107349540 4272690 0.03980166100385712 0.3136524653104425 chr15 102531392 3847439 0.037524497863054465 0.22655622640013168 chr16 90354753 3914847 0.04332751593045692 0.2813136608524293 chr17 81195210 3832876 0.04720569107463359 0.2823991364265376 chr18 78077248 3994436 0.05116005113294977 1.0010533399617845 chr19 59128983 2899925 0.04904405340440237 0.5956738222184355 chr20 63025520 2726445 0.04325938127920246 0.25248676432878847 chr21 48129895 1789827 0.0371874278969443 0.24417476622810247 chr22 51304566 1509240 0.029417264732343705 0.1948059383947069 chrMT 16571 34869 2.1042182125399793 2.1447686796564778 chrX 155270560 7388418 0.047584152462643275 0.35356344187076116 chrY 59373566 354223 0.005966005141075744 0.16569106310489135