BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717078.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 = 513,492 number of mapped reads = 414,195 (80.66%) number of supplementary alignments = 958 (0.19%) number of secondary alignments = 0 number of mapped bases = 24,182,162 bp number of sequenced bases = 24,174,352 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,125 duplication rate = 1.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9461 >>>>>>> ACTG content number of A's = 5,880,025 bp (24.32%) number of C's = 4,468,283 bp (18.48%) number of T's = 7,785,208 bp (32.2%) number of G's = 6,040,562 bp (24.99%) number of N's = 274 bp (0%) GC percentage = 43.47% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 117,324 number of insertions = 1,531 mapped reads with insertion percentage = 0.37% number of deletions = 4,881 mapped reads with deletion percentage = 1.17% homopolymer indels = 42.86% >>>>>>> Coverage mean coverageData = 0.0078X std coverageData = 0.1057X There is a 0.75% of reference with a coverageData >= 1X There is a 0.02% 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 3069660 0.01231555607638787 0.14297689846188572 chr2 243199373 2492613 0.010249257509393333 0.1292974968318058 chr3 198022430 1645449 0.008309407171702721 0.09527997500999155 chr4 191154276 900637 0.004711571296474686 0.07263002665928754 chr5 180915260 1725103 0.00953542006351482 0.10041203534532024 chr6 171115067 953638 0.005573080247807751 0.08072356346695378 chr7 159138663 1646593 0.010346907338287742 0.15394587923821912 chr8 146364022 868424 0.005933316044020709 0.08717443485217924 chr9 141213431 689271 0.004881058374681088 0.0845135639743092 chr10 135534747 1182465 0.008724441710877285 0.1304296941341137 chr11 135006516 999050 0.007400013196400091 0.10120878663413456 chr12 133851895 961922 0.007186465309288299 0.087062979650295 chr13 115169878 594753 0.005164136754577443 0.07385148232012793 chr14 107349540 546221 0.005088247234221963 0.07411649963912854 chr15 102531392 1043056 0.010173040467450203 0.10399761169832612 chr16 90354753 714117 0.007903480185486202 0.09685063019831862 chr17 81195210 881378 0.010855049207952045 0.10917990340656795 chr18 78077248 790542 0.010125126336420055 0.14706662198316622 chr19 59128983 366169 0.006192716015426817 0.1188869560553821 chr20 63025520 621769 0.009865352955437733 0.10220641484502685 chr21 48129895 295223 0.006133879992881763 0.08157475265783246 chr22 51304566 294748 0.005745063704466382 0.07783747040828766 chrMT 16571 1071 0.06463098183573714 0.27242025355678073 chrX 155270560 843398 0.0054317959566836105 0.08155307665286321 chrY 59373566 54892 9.245191707030028E-4 0.03691361595051917