BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525122.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 = 953,474 number of mapped reads = 860,434 (90.24%) number of supplementary alignments = 24,388 (2.56%) number of secondary alignments = 0 number of mapped bases = 65,916,415 bp number of sequenced bases = 65,890,383 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,970 duplication rate = 1.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8699 >>>>>>> ACTG content number of A's = 17,389,603 bp (26.39%) number of C's = 13,113,481 bp (19.9%) number of T's = 20,025,104 bp (30.39%) number of G's = 15,359,747 bp (23.31%) number of N's = 2,448 bp (0%) GC percentage = 43.21% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 496,637 number of insertions = 5,739 mapped reads with insertion percentage = 0.66% number of deletions = 15,191 mapped reads with deletion percentage = 1.74% homopolymer indels = 42.67% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 0.2349X There is a 1.96% of reference with a coverageData >= 1X There is a 0.11% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 5260399 0.0211048581499823 0.336518446041299 chr2 243199373 5703385 0.02345147904637073 0.3432105793843765 chr3 198022430 4325661 0.02184429814339719 0.1556609894021281 chr4 191154276 4230389 0.022130757880613666 0.16169614451629366 chr5 180915260 3993547 0.022074130175641346 0.1590931589530014 chr6 171115067 3838078 0.02242980742309501 0.17428342741599018 chr7 159138663 3670369 0.023063967805234106 0.33972138970024446 chr8 146364022 3385360 0.023129727878071018 0.2993198493590305 chr9 141213431 2785994 0.01972895906763996 0.2275555290432577 chr10 135534747 3125658 0.02306167288599432 0.2268074210171176 chr11 135006516 2987445 0.02212815416998095 0.22293201030553497 chr12 133851895 2975691 0.022231220559111246 0.15828818034111475 chr13 115169878 2079985 0.018060147636867342 0.14084568853544396 chr14 107349540 1977466 0.01842081484466538 0.16026371338658615 chr15 102531392 1901507 0.018545607963656632 0.1440114963146521 chr16 90354753 1896111 0.0209851827053304 0.16335844287681572 chr17 81195210 1787340 0.022012874897423138 0.1766853162029173 chr18 78077248 1822520 0.023342523547961118 0.3832364423259422 chr19 59128983 1371500 0.023195054783878153 0.2946470889444383 chr20 63025520 1336637 0.021207869447169972 0.1558304004859441 chr21 48129895 856182 0.017788985411250118 0.14785433644045534 chr22 51304566 719512 0.01402432680163399 0.1244688289873293 chrMT 16571 2180 0.13155512642568343 0.3700521816255416 chrX 155270560 3727639 0.024007377831315867 0.1993260202341876 chrY 59373566 155860 0.002625073925995956 0.07291364590688618