BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173883.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 1,768,978 number of mapped reads = 1,725,961 (97.57%) number of supplementary alignments = 174,102 (9.84%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 863,910 number of mapped paired reads (second in pair) = 862,051 number of mapped paired reads (both in pair) = 1,698,638 number of mapped paired reads (singletons) = 27,323 number of mapped bases = 204,467,371 bp number of sequenced bases = 204,344,856 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,298,930 duplication rate = 62.71% >>>>>>> Insert size mean insert size = 1,049,875.5338 std insert size = 9,621,672.9225 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 53.0044 >>>>>>> ACTG content number of A's = 62,177,104 bp (30.43%) number of C's = 39,368,869 bp (19.27%) number of T's = 61,942,069 bp (30.31%) number of G's = 40,854,358 bp (19.99%) number of N's = 2,456 bp (0%) GC percentage = 39.26% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 2,092,541 number of insertions = 23,453 mapped reads with insertion percentage = 1.31% number of deletions = 51,209 mapped reads with deletion percentage = 2.9% homopolymer indels = 42.47% >>>>>>> Coverage mean coverageData = 0.066X std coverageData = 1.1191X There is a 1.53% of reference with a coverageData >= 1X There is a 1.15% of reference with a coverageData >= 2X There is a 0.85% of reference with a coverageData >= 3X There is a 0.68% of reference with a coverageData >= 4X There is a 0.5% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.29% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.17% of reference with a coverageData >= 9X There is a 0.14% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.07% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 16529992 0.06631875954282979 0.8760009061455644 chr2 243199373 18051052 0.07422326701475501 2.894953548958694 chr3 198022430 13771741 0.06954636906536295 0.744539217820952 chr4 191154276 14632171 0.07654639648238891 0.8923607882237213 chr5 180915260 13554020 0.07491916381183102 0.7757045716239639 chr6 171115067 12032842 0.07032017817577689 0.7888443686069587 chr7 159138663 11084819 0.06965509695151831 0.8248439631978217 chr8 146364022 10512844 0.07182669522432228 0.9423020347478094 chr9 141213431 9094484 0.06440240093026278 0.8635079058969847 chr10 135534747 9726266 0.07176215852603465 1.000120515210417 chr11 135006516 9652494 0.07149650465759741 0.7583172883272737 chr12 133851895 9313140 0.06957794658043503 0.738887985895852 chr13 115169878 6872176 0.05966990778613137 0.7013820967386177 chr14 107349540 6333074 0.05899488716952117 0.6919348082756946 chr15 102531392 5827913 0.05684027970672631 0.6597066304402658 chr16 90354753 6084317 0.06733809565059627 0.7965234545428687 chr17 81195210 5240370 0.06454038360144644 0.733081112493407 chr18 78077248 5889181 0.07542762009234752 1.054424153315146 chr19 59128983 3337673 0.05644732634755446 0.6938426955638647 chr20 63025520 4040285 0.06410554010502412 0.7193285875953 chr21 48129895 2765462 0.05745830112448822 0.8172183021425684 chr22 51304566 2268876 0.04422366617427385 0.6224877708370854 chrMT 16571 462478 27.90887695371432 21.792572015741396 chrX 155270560 5762308 0.037111400899178824 0.5398781223416663 chrY 59373566 1627393 0.027409386190480795 0.5869396337078903