BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525042.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 = 684,436 number of mapped reads = 623,879 (91.15%) number of supplementary alignments = 2,534 (0.37%) number of secondary alignments = 0 number of mapped bases = 35,983,339 bp number of sequenced bases = 35,971,810 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,038 duplication rate = 1.4% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8073 >>>>>>> ACTG content number of A's = 9,128,263 bp (25.38%) number of C's = 6,423,108 bp (17.86%) number of T's = 11,247,752 bp (31.27%) number of G's = 9,172,298 bp (25.5%) number of N's = 389 bp (0%) GC percentage = 43.35% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 174,535 number of insertions = 2,450 mapped reads with insertion percentage = 0.39% number of deletions = 6,850 mapped reads with deletion percentage = 1.09% homopolymer indels = 42.97% >>>>>>> Coverage mean coverageData = 0.0116X std coverageData = 0.134X There is a 1.1% of reference with a coverageData >= 1X There is a 0.04% 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 2970812 0.011918975319222976 0.2050952954009721 chr2 243199373 2956104 0.012155064232011814 0.14506419161103265 chr3 198022430 2479895 0.012523303546976977 0.11716436586223175 chr4 191154276 2375695 0.012428155151496584 0.12246970765006532 chr5 180915260 2203983 0.012182405176876732 0.11480731050827996 chr6 171115067 2115603 0.012363627803739808 0.12513918524872517 chr7 159138663 2018084 0.012681292917485426 0.15894903752803197 chr8 146364022 1893279 0.012935412501851035 0.13803565168932605 chr9 141213431 1502527 0.0106401139704622 0.11812646043753401 chr10 135534747 1807124 0.013333289359369963 0.14702279425852696 chr11 135006516 1719892 0.012739325855946095 0.1321089646428113 chr12 133851895 1687344 0.012606052383494458 0.11734434977834157 chr13 115169878 1186960 0.010306167034404604 0.10549617676871037 chr14 107349540 1130577 0.010531735860256132 0.10789970383666245 chr15 102531392 1076552 0.010499730658099326 0.10804297844002785 chr16 90354753 1112267 0.012309999895633604 0.1191617127637386 chr17 81195210 1017957 0.012537155824832525 0.12066360569823427 chr18 78077248 982748 0.012586867815832853 0.17302931591623205 chr19 59128983 771806 0.013052921948615284 0.15011872062610174 chr20 63025520 800230 0.01269692023167758 0.11827589393014035 chr21 48129895 480854 0.009990755226039866 0.10872427644828138 chr22 51304566 433654 0.00845254202130859 0.09489341286887382 chrMT 16571 5662 0.3416812503771649 0.6182060768194743 chrX 155270560 1154240 0.007433733735487268 0.09510009514035746 chrY 59373566 99490 0.0016756615225031288 0.0604662231397511