BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524805.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 = 1,505,998 number of mapped reads = 1,369,382 (90.93%) number of supplementary alignments = 5,217 (0.35%) number of secondary alignments = 0 number of mapped bases = 78,208,001 bp number of sequenced bases = 78,183,072 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,554 duplication rate = 3.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3362 >>>>>>> ACTG content number of A's = 19,532,044 bp (24.98%) number of C's = 15,083,270 bp (19.29%) number of T's = 24,728,125 bp (31.63%) number of G's = 18,830,505 bp (24.09%) number of N's = 9,128 bp (0.01%) GC percentage = 43.38% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 397,656 number of insertions = 4,932 mapped reads with insertion percentage = 0.36% number of deletions = 15,450 mapped reads with deletion percentage = 1.12% homopolymer indels = 42.98% >>>>>>> Coverage mean coverageData = 0.0253X std coverageData = 0.2375X There is a 2.25% of reference with a coverageData >= 1X There is a 0.2% 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 6272181 0.02516415395410389 0.3195519335429624 chr2 243199373 6566140 0.026999000527850866 0.39466778984273115 chr3 198022430 5123363 0.025872639781261142 0.17942595950461113 chr4 191154276 5070088 0.026523539551895767 0.20616911392931278 chr5 180915260 4685587 0.025899346467511918 0.1776629029912408 chr6 171115067 4463586 0.02608528914639644 0.20300203104711884 chr7 159138663 4342482 0.027287410351059693 0.2765046476331872 chr8 146364022 3866869 0.026419532253629925 0.22129587441261916 chr9 141213431 3314874 0.023474211882862615 0.2024970676538553 chr10 135534747 3879325 0.028622365008730933 0.2847169344080694 chr11 135006516 3527271 0.026126672285951 0.20432931956922887 chr12 133851895 3502434 0.026166487967914088 0.18051583643123292 chr13 115169878 2416192 0.020979374485401468 0.16071218813747548 chr14 107349540 2152494 0.020051264309097178 0.16157566977709756 chr15 102531392 2275212 0.022190394138021652 0.16479948944543343 chr16 90354753 2369200 0.026221088778805027 0.19688449735296631 chr17 81195210 2223393 0.02738330253718169 0.18930175626569967 chr18 78077248 2026979 0.02596119934964921 0.2847771510722673 chr19 59128983 1761311 0.029787608557380395 0.2737028415324319 chr20 63025520 1661249 0.02635835452051804 0.18734428467155448 chr21 48129895 1050151 0.021819100166331134 0.17969966495240083 chr22 51304566 973297 0.018970962545516903 0.15428382717400385 chrMT 16571 27880 1.6824573049303 1.5670753242837232 chrX 155270560 4382703 0.028226232970371204 0.19677860340160908 chrY 59373566 273740 0.004610469244848794 0.13645612381003505