BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354875.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 23,293,756 number of mapped reads = 23,059,629 (98.99%) number of supplementary alignments = 1,223,576 (5.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,540,599 number of mapped paired reads (second in pair) = 11,519,030 number of mapped paired reads (both in pair) = 23,018,564 number of mapped paired reads (singletons) = 41,065 number of mapped bases = 2,775,021,191 bp number of sequenced bases = 2,773,664,571 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,815,136 duplication rate = 62.83% >>>>>>> Insert size mean insert size = 522,544.7965 std insert size = 8,351,465.3784 median insert size = 141 >>>>>>> Mapping quality mean mapping quality = 53.3855 >>>>>>> ACTG content number of A's = 745,349,970 bp (26.87%) number of C's = 609,438,539 bp (21.97%) number of T's = 764,989,212 bp (27.58%) number of G's = 653,805,626 bp (23.57%) number of N's = 81,224 bp (0%) GC percentage = 45.54% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 15,900,939 number of insertions = 449,438 mapped reads with insertion percentage = 1.8% number of deletions = 451,497 mapped reads with deletion percentage = 1.85% homopolymer indels = 41.75% >>>>>>> Coverage mean coverageData = 0.8964X std coverageData = 61.4159X There is a 23.64% of reference with a coverageData >= 1X There is a 19.27% of reference with a coverageData >= 2X There is a 11.24% of reference with a coverageData >= 3X There is a 9.42% of reference with a coverageData >= 4X There is a 5.39% of reference with a coverageData >= 5X There is a 4.6% of reference with a coverageData >= 6X There is a 2.62% of reference with a coverageData >= 7X There is a 2.25% of reference with a coverageData >= 8X There is a 1.29% of reference with a coverageData >= 9X There is a 1.1% of reference with a coverageData >= 10X There is a 0.64% of reference with a coverageData >= 11X There is a 0.55% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.15% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.09% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.06% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 226828559 0.9100421017607013 26.165665930835246 chr2 243199373 272086198 1.1187783695478524 213.90077423655453 chr3 198022430 173478504 0.8760548186384745 3.0349523869495916 chr4 191154276 181756940 0.9508389966646627 14.369750185018182 chr5 180915260 156944163 0.8675009670273254 2.1029996375852384 chr6 171115067 153157906 0.8950579787342747 4.167979970177764 chr7 159138663 148251115 0.9315845200986764 18.713440381618746 chr8 146364022 131997033 0.9018407064544864 3.8247260452598013 chr9 141213431 118376887 0.838283484522092 11.095213094469093 chr10 135534747 159413768 1.1761837575127505 37.12509662711229 chr11 135006516 127691857 0.9458199558308726 5.283293984044658 chr12 133851895 120046188 0.8968583373436738 2.144746856246175 chr13 115169878 82908664 0.7198814954028171 1.8769675097161524 chr14 107349540 84316759 0.7854412697064188 8.415417569986484 chr15 102531392 81168898 0.7916492346070948 1.976490929786906 chr16 90354753 90674050 1.0035338152050508 6.6452373872122035 chr17 81195210 81573607 1.004660336490293 6.237361084955706 chr18 78077248 73635656 0.9431128515185371 11.821483239140537 chr19 59128983 60764972 1.02766814034329 14.444363134730967 chr20 63025520 60937060 0.9668632642777084 5.373119239506773 chr21 48129895 40035496 0.831821802229155 8.443721808676798 chr22 51304566 38144656 0.7434943704620754 3.1587593678563857 chrMT 16571 3377740 203.8344095105908 64.43625583355997 chrX 155270560 71406944 0.4598872059197829 2.237283655498415 chrY 59373566 36047571 0.6071316484510969 18.87113198642789