BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716111.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 = 2,432,866 number of mapped reads = 2,056,472 (84.53%) number of supplementary alignments = 7,057 (0.29%) number of secondary alignments = 0 number of mapped bases = 116,089,567 bp number of sequenced bases = 116,054,703 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,440 duplication rate = 2.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.8668 >>>>>>> ACTG content number of A's = 28,927,689 bp (24.93%) number of C's = 22,439,079 bp (19.33%) number of T's = 36,768,857 bp (31.68%) number of G's = 27,918,183 bp (24.06%) number of N's = 895 bp (0%) GC percentage = 43.39% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 609,119 number of insertions = 7,459 mapped reads with insertion percentage = 0.36% number of deletions = 21,931 mapped reads with deletion percentage = 1.06% homopolymer indels = 41.16% >>>>>>> Coverage mean coverageData = 0.0375X std coverageData = 0.305X There is a 3.31% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9758340 0.039150714894307125 0.37285166335413555 chr2 243199373 9068311 0.037287559125409424 0.5132379668761546 chr3 198022430 6747731 0.0340755893158164 0.21026588938794843 chr4 191154276 7064790 0.036958576851296804 0.23279183729635658 chr5 180915260 6584928 0.03639785831222861 0.2111287852972168 chr6 171115067 6190796 0.03617914020394242 0.2601503058307918 chr7 159138663 6611120 0.04154314153060341 0.42948311149617996 chr8 146364022 5976044 0.0408300067075227 0.27814018754868874 chr9 141213431 3864755 0.027368182846573566 0.2201313143696506 chr10 135534747 5106457 0.037676367964888 0.37312878396839844 chr11 135006516 4121661 0.030529348672326304 0.25776712363360477 chr12 133851895 5787895 0.04324103891095453 0.23260905434220486 chr13 115169878 3458604 0.03003045640110863 0.1939200733174456 chr14 107349540 3908937 0.036413169539431654 0.2263111091256087 chr15 102531392 4273393 0.04167887431002595 0.23144998964876864 chr16 90354753 4064897 0.04498819226477217 0.25559637247710865 chr17 81195210 5218415 0.06426998587724571 0.30269493311923407 chr18 78077248 2115422 0.027093962123255162 0.3463223404350671 chr19 59128983 3153650 0.05333509625896999 0.3635579670045522 chr20 63025520 3718201 0.05899516576777153 0.2848612766318766 chr21 48129895 1434006 0.029794496746772457 0.21164659595622215 chr22 51304566 1103486 0.021508533957776778 0.16364094478968028 chrMT 16571 155017 9.354716070243196 6.758079046239518 chrX 155270560 6251787 0.040263827218759304 0.24569958339504097 chrY 59373566 350924 0.005910441693867605 0.1638640228278229