BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716447.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 = 456,465 number of mapped reads = 384,517 (84.24%) number of supplementary alignments = 5,846 (1.28%) number of secondary alignments = 0 number of mapped bases = 29,835,585 bp number of sequenced bases = 29,822,672 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,219 duplication rate = 1.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3122 >>>>>>> ACTG content number of A's = 7,507,703 bp (25.17%) number of C's = 5,818,714 bp (19.51%) number of T's = 9,247,564 bp (31.01%) number of G's = 7,247,212 bp (24.3%) number of N's = 1,479 bp (0%) GC percentage = 43.81% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 258,594 number of insertions = 2,886 mapped reads with insertion percentage = 0.74% number of deletions = 7,447 mapped reads with deletion percentage = 1.91% homopolymer indels = 43.99% >>>>>>> Coverage mean coverageData = 0.0096X std coverageData = 0.1467X There is a 0.9% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 2385125 0.009569183781491963 0.2050355699516986 chr2 243199373 2513833 0.010336511023817484 0.2025914180392493 chr3 198022430 1947710 0.009835804964114419 0.10246926372162293 chr4 191154276 1865401 0.009758615078011647 0.1065546484442883 chr5 180915260 1776272 0.00981825413732374 0.1027655953181956 chr6 171115067 1691882 0.009887393492941215 0.11227783634333363 chr7 159138663 1675523 0.010528698484792473 0.18207866369761994 chr8 146364022 1527061 0.01043330853534484 0.18452727554917636 chr9 141213431 1275552 0.009032795187874162 0.16052289285620416 chr10 135534747 1417906 0.010461568205826954 0.1497414483098302 chr11 135006516 1359446 0.010069484349925746 0.1494111833041512 chr12 133851895 1357629 0.010142770111696961 0.10607819118819904 chr13 115169878 913196 0.007929121883762002 0.0914244968797545 chr14 107349540 919903 0.008569230944072978 0.11650631097182115 chr15 102531392 852169 0.00831129845579391 0.09457412334649908 chr16 90354753 867616 0.009602328280394945 0.10925334766274127 chr17 81195210 843952 0.010394110687071318 0.1101535893816691 chr18 78077248 829965 0.010630049358297054 0.25994594032656065 chr19 59128983 669281 0.01131900070055323 0.16439541992610385 chr20 63025520 620196 0.00984039481149858 0.10571264613758519 chr21 48129895 386625 0.008032949168079423 0.09622289874405116 chr22 51304566 358169 0.006981230481513088 0.08592687533120885 chrMT 16571 1080 0.0651740993301551 0.2683843727717618 chrX 155270560 1695793 0.01092153593057177 0.12512494552413908 chrY 59373566 84300 0.0014198237646699543 0.05282210057572426