BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716852.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 = 627,240 number of mapped reads = 576,774 (91.95%) number of supplementary alignments = 2,926 (0.47%) number of secondary alignments = 0 number of mapped bases = 33,720,023 bp number of sequenced bases = 33,710,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,825 duplication rate = 2.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9308 >>>>>>> ACTG content number of A's = 8,625,251 bp (25.59%) number of C's = 7,027,073 bp (20.85%) number of T's = 10,087,831 bp (29.93%) number of G's = 7,970,006 bp (23.64%) number of N's = 195 bp (0%) GC percentage = 44.49% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 165,942 number of insertions = 2,590 mapped reads with insertion percentage = 0.45% number of deletions = 6,063 mapped reads with deletion percentage = 1.04% homopolymer indels = 41.84% >>>>>>> Coverage mean coverageData = 0.0109X std coverageData = 0.1289X There is a 1.02% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% 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 3969716 0.015926604251068247 0.184669345953667 chr2 243199373 3400598 0.013982758088771882 0.16511493286099999 chr3 198022430 2103428 0.010622170427865167 0.10811761607632582 chr4 191154276 1537745 0.00804452315782881 0.10268403901002636 chr5 180915260 2420689 0.013380236692029186 0.12155167705557685 chr6 171115067 1230531 0.007191248681800768 0.0920371725592175 chr7 159138663 2249764 0.01413713020826372 0.1754341255338714 chr8 146364022 1510162 0.010317849833342241 0.12070604973141397 chr9 141213431 934241 0.006615808378737005 0.10112317636367396 chr10 135534747 1508250 0.011128142659977814 0.1285452377036163 chr11 135006516 1428750 0.010582822535765608 0.12258523221430853 chr12 133851895 1278027 0.009548068034449568 0.10269458980231898 chr13 115169878 957558 0.008314309406492556 0.09547515961961273 chr14 107349540 713002 0.006641872894844263 0.08786943252868908 chr15 102531392 1462742 0.014266284417556722 0.12505711025656482 chr16 90354753 1025690 0.011351810125583542 0.1142504347024913 chr17 81195210 1292431 0.01591757691124883 0.13829729824667455 chr18 78077248 1076413 0.01378651306972295 0.18807761121363756 chr19 59128983 555547 0.009395510827575032 0.12754970668393562 chr20 63025520 907619 0.0144008173197143 0.1264113218242981 chr21 48129895 424904 0.008828276064180069 0.10167755762904772 chr22 51304566 390832 0.007617879469051546 0.09162492752161303 chrMT 16571 35607 2.148753847082252 1.940864544509859 chrX 155270560 1217930 0.007843920959646181 0.09667302082528266 chrY 59373566 87847 0.0014795641548631254 0.05298932644636639