BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714061.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 308,500 number of mapped reads = 255,899 (82.95%) number of supplementary alignments = 9,178 (2.98%) number of secondary alignments = 0 number of mapped bases = 32,933,573 bp number of sequenced bases = 32,306,244 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 195,432 duplication rate = 41.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 52.5283 >>>>>>> ACTG content number of A's = 8,907,615 bp (27.57%) number of C's = 7,036,150 bp (21.78%) number of T's = 8,462,659 bp (26.2%) number of G's = 7,899,581 bp (24.45%) number of N's = 239 bp (0%) GC percentage = 46.23% >>>>>>> Mismatches and indels general error rate = 0.042 number of mismatches = 1,242,856 number of insertions = 36,366 mapped reads with insertion percentage = 13.78% number of deletions = 108,470 mapped reads with deletion percentage = 40.52% homopolymer indels = 28.51% >>>>>>> Coverage mean coverageData = 0.0106X std coverageData = 1.2217X There is a 0.05% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3060074 0.012277096794073785 1.307194771841503 chr2 243199373 3209953 0.013198853929611077 2.3085304272271414 chr3 198022430 1667542 0.008420975341025762 0.7764463616419417 chr4 191154276 1584766 0.00829050771534925 0.9433131338017802 chr5 180915260 1811227 0.010011466141662125 0.9363222269726661 chr6 171115067 1326292 0.007750877951618369 0.7495113377335202 chr7 159138663 1254234 0.007881390834608181 0.7874697919717512 chr8 146364022 1449482 0.009903267074746005 1.1093125740270375 chr9 141213431 1276709 0.009040988459518414 0.9214438353782569 chr10 135534747 1906005 0.014062851351321739 1.3017439082857643 chr11 135006516 1503934 0.011139714174981006 1.095514280569184 chr12 133851895 1374429 0.010268281969411042 0.9921831199670329 chr13 115169878 874466 0.007592836036519896 0.9738186282752994 chr14 107349540 1118336 0.010417706494131228 1.1242740597159249 chr15 102531392 955792 0.009321945029284299 0.8559515957368705 chr16 90354753 1167970 0.01292649209057104 1.3349056716623133 chr17 81195210 1221344 0.015042069599918518 1.551905468152587 chr18 78077248 760345 0.009738368340031656 0.8776069039037911 chr19 59128983 769818 0.013019300534900118 1.4174892891282433 chr20 63025520 893222 0.014172386042987031 1.1810468726902865 chr21 48129895 265313 0.005512436709034998 0.5279184482903367 chr22 51304566 421505 0.008215740485944272 0.8918642900635771 chrMT 16571 200152 12.07845030474926 110.05229926997339 chrX 155270560 2760804 0.01778060180886834 1.2098984822697971 chrY 59373566 99859 0.0016818764094445667 0.26955489981743086