BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524515.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 = 1,124,212 number of mapped reads = 1,032,537 (91.85%) number of supplementary alignments = 4,082 (0.36%) number of secondary alignments = 0 number of mapped bases = 60,402,404 bp number of sequenced bases = 60,383,456 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,176 duplication rate = 4.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0237 >>>>>>> ACTG content number of A's = 14,980,202 bp (24.81%) number of C's = 11,404,193 bp (18.89%) number of T's = 19,373,772 bp (32.08%) number of G's = 14,624,393 bp (24.22%) number of N's = 896 bp (0%) GC percentage = 43.11% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 309,021 number of insertions = 4,891 mapped reads with insertion percentage = 0.47% number of deletions = 11,219 mapped reads with deletion percentage = 1.08% homopolymer indels = 40.38% >>>>>>> Coverage mean coverageData = 0.0195X std coverageData = 0.2114X There is a 1.71% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5763149 0.023121904278023846 0.3665598287732594 chr2 243199373 4685753 0.019267126153322774 0.2582937148732117 chr3 198022430 3538504 0.01786920804880538 0.14939213817590102 chr4 191154276 3714236 0.019430567171827222 0.18040556768961621 chr5 180915260 3217520 0.01778467996563695 0.14993713302599468 chr6 171115067 2509117 0.014663331780128982 0.15637283546247085 chr7 159138663 2947159 0.01851944049573924 0.23392628178017458 chr8 146364022 5285736 0.036113629072040666 0.24890980073173666 chr9 141213431 2508542 0.017764188450318158 0.1738609726007375 chr10 135534747 3548733 0.026183197139844884 0.24776579310589011 chr11 135006516 2000495 0.01481776627729583 0.17168386124000568 chr12 133851895 2715829 0.02028980613236742 0.16006767529437754 chr13 115169878 1291225 0.011211481877231822 0.1174846681268323 chr14 107349540 1397278 0.013016152654217242 0.12828939637461206 chr15 102531392 1550435 0.015121563940144302 0.13662662403287215 chr16 90354753 1852558 0.020503160470152576 0.16843922720429558 chr17 81195210 2036054 0.025076035889309234 0.18487689830649331 chr18 78077248 1839295 0.0235573748705897 0.28495763268526014 chr19 59128983 1229944 0.020801034240687008 0.27474155734215805 chr20 63025520 1708664 0.02711066882113785 0.1871918079212241 chr21 48129895 820729 0.017052374620804802 0.16390476743573673 chr22 51304566 483863 0.009431187859575696 0.10732714220074038 chrMT 16571 2717 0.163961136925955 0.40580287193111586 chrX 155270560 3518916 0.02266312429091516 0.17863812878470048 chrY 59373566 235953 0.003974041242528704 0.15109425941726007