BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716548.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 = 1,351,227 number of mapped reads = 1,046,947 (77.48%) number of supplementary alignments = 1,648 (0.12%) number of secondary alignments = 0 number of mapped bases = 56,530,135 bp number of sequenced bases = 56,514,875 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,566 duplication rate = 4.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2256 >>>>>>> ACTG content number of A's = 12,997,191 bp (23%) number of C's = 9,821,135 bp (17.38%) number of T's = 18,027,623 bp (31.9%) number of G's = 15,667,961 bp (27.72%) number of N's = 965 bp (0%) GC percentage = 45.1% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 385,049 number of insertions = 4,192 mapped reads with insertion percentage = 0.4% number of deletions = 9,037 mapped reads with deletion percentage = 0.86% homopolymer indels = 38.88% >>>>>>> Coverage mean coverageData = 0.0183X std coverageData = 0.1757X There is a 1.63% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 5466006 0.0219297588028878 0.22853045935146213 chr2 243199373 4813002 0.019790355298325544 0.25184055651000403 chr3 198022430 3800593 0.019192739933551972 0.15219151343224976 chr4 191154276 3655762 0.019124667658493813 0.16257599758036814 chr5 180915260 3436730 0.018996352214843568 0.1516951013854449 chr6 171115067 2410483 0.014086912638733327 0.14642081417903446 chr7 159138663 3235967 0.020334260317368635 0.19881012414744617 chr8 146364022 3470774 0.023713300253528153 0.17778711217472387 chr9 141213431 2527927 0.01790146292812615 0.16097346463101359 chr10 135534747 2830916 0.020887012833690537 0.19188124261072712 chr11 135006516 2351730 0.017419381446744393 0.16628326665957924 chr12 133851895 2649719 0.019795902030374693 0.15526685169537063 chr13 115169878 958675 0.008324008123026751 0.10094130158953833 chr14 107349540 2679525 0.024960749715369063 0.17532136521408168 chr15 102531392 1048144 0.010222664293877918 0.11144562487785863 chr16 90354753 1387600 0.015357244128596091 0.14640808158497032 chr17 81195210 2150760 0.02648875469378058 0.18705447555872928 chr18 78077248 1528162 0.019572436774410902 0.20759610941491335 chr19 59128983 1352899 0.022880471324866182 0.20281071353276622 chr20 63025520 1407517 0.02233249325035319 0.1704536126252123 chr21 48129895 774479 0.016091433401215605 0.1476515819728243 chr22 51304566 571427 0.011137936533758028 0.11631700729023178 chrMT 16571 53994 3.2583428881781424 2.8105648734358533 chrX 155270560 1800682 0.01159705999643461 0.12641165257249645 chrY 59373566 166662 0.0028070067410133326 0.08266899315816324