BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124919.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 5,274,710 number of mapped reads = 5,144,696 (97.54%) number of supplementary alignments = 5,156 (0.1%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,602,434 number of mapped paired reads (second in pair) = 2,542,262 number of mapped paired reads (both in pair) = 5,068,256 number of mapped paired reads (singletons) = 76,440 number of mapped bases = 319,359,937 bp number of sequenced bases = 319,226,430 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 281,448 duplication rate = 3.88% >>>>>>> Insert size mean insert size = 25,953.5806 std insert size = 1,542,906.9294 median insert size = 197 >>>>>>> Mapping quality mean mapping quality = 52.0409 >>>>>>> ACTG content number of A's = 87,344,862 bp (27.36%) number of C's = 57,193,330 bp (17.92%) number of T's = 95,300,859 bp (29.85%) number of G's = 79,384,787 bp (24.87%) number of N's = 2,592 bp (0%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0068 number of mismatches = 2,099,388 number of insertions = 33,070 mapped reads with insertion percentage = 0.64% number of deletions = 91,158 mapped reads with deletion percentage = 1.75% homopolymer indels = 48.46% >>>>>>> Coverage mean coverageData = 0.1032X std coverageData = 0.7707X There is a 8.19% of reference with a coverageData >= 1X There is a 1.41% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.09% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 31026471 0.12447901182962348 0.8519944044108754 chr2 243199373 25670636 0.10555387410476588 0.7897578520566154 chr3 198022430 25808102 0.1303291854362155 0.43680372183470534 chr4 191154276 18274359 0.0956000534353728 0.46838355194487097 chr5 180915260 14806480 0.08184207346577618 0.3363910525419813 chr6 171115067 22055187 0.12889097019142096 0.9315264605147398 chr7 159138663 15958016 0.100277429124813 0.9451163982320826 chr8 146364022 25454354 0.17391127718531812 0.6202862747190013 chr9 141213431 14575262 0.10321441733116732 0.7091802257414853 chr10 135534747 12479838 0.09207851326863066 1.9408264503659762 chr11 135006516 14358934 0.10635734055976973 0.7604743347246484 chr12 133851895 13929233 0.10406451847394466 0.38432120858437174 chr13 115169878 10911588 0.0947434189345933 0.3617376003711525 chr14 107349540 8790101 0.0818829871092135 0.38414902772694265 chr15 102531392 6623292 0.06459769901495144 0.30797918609824926 chr16 90354753 5961345 0.06597710471301936 0.7335788598575034 chr17 81195210 6954285 0.08564895638548135 0.908372125769739 chr18 78077248 10186454 0.13046635557646705 1.1614651942200973 chr19 59128983 5633219 0.09527001335368816 0.720214392651215 chr20 63025520 8338750 0.13230751606650767 0.4512717318471184 chr21 48129895 4461553 0.09269816607744522 0.40828079962167557 chr22 51304566 3475414 0.06774083226822346 0.30958769374055484 chrMT 16571 49673 2.9975861444692535 2.6041833372344825 chrX 155270560 12952552 0.08341923929430022 0.5540058635786635 chrY 59373566 624839 0.010523858378322771 0.4389900680682073