BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080665.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,264,749 number of mapped reads = 1,154,560 (91.29%) number of supplementary alignments = 13,954 (1.1%) number of secondary alignments = 0 number of mapped bases = 77,155,010 bp number of sequenced bases = 77,126,673 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,701 duplication rate = 2.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6613 >>>>>>> ACTG content number of A's = 21,178,563 bp (27.46%) number of C's = 14,393,816 bp (18.66%) number of T's = 24,226,790 bp (31.41%) number of G's = 17,324,177 bp (22.46%) number of N's = 3,327 bp (0%) GC percentage = 41.12% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 509,999 number of insertions = 5,759 mapped reads with insertion percentage = 0.5% number of deletions = 17,513 mapped reads with deletion percentage = 1.5% homopolymer indels = 47.84% >>>>>>> Coverage mean coverageData = 0.0249X std coverageData = 0.2025X There is a 2.2% of reference with a coverageData >= 1X There is a 0.24% of reference with a coverageData >= 2X There is a 0.03% 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 9312804 0.037363212828264124 0.25041701547357414 chr2 243199373 5173409 0.021272295796584968 0.26791939112060703 chr3 198022430 4720730 0.023839370115799507 0.17043136585351318 chr4 191154276 3255432 0.017030390677737182 0.1462966870672272 chr5 180915260 3469146 0.019175530024388213 0.15257189269919125 chr6 171115067 4505853 0.026332298370896817 0.20382472639618543 chr7 159138663 4660617 0.02928651599894364 0.30118560289632496 chr8 146364022 8991412 0.06143184559385776 0.29606997891246606 chr9 141213431 2359685 0.016710060674044524 0.1632696047543629 chr10 135534747 3687779 0.027209103802731855 0.18877516965810573 chr11 135006516 3139043 0.023251048119781122 0.17772123267220447 chr12 133851895 2434247 0.018186122803864675 0.1495634188037872 chr13 115169878 1478545 0.012837948825473271 0.1257611827520165 chr14 107349540 1489035 0.013870902474290995 0.13075300046042884 chr15 102531392 1410228 0.01375410957065715 0.13357728911615027 chr16 90354753 1851361 0.020489912688931817 0.1609307656357614 chr17 81195210 1299902 0.016009589728261064 0.1421329938777483 chr18 78077248 2402154 0.030766376396873005 0.24011793434675066 chr19 59128983 1228494 0.02077651157977806 0.18496763756550202 chr20 63025520 1955038 0.031019783732050128 0.19588476489290685 chr21 48129895 1160100 0.02410352235341465 0.17328072210876388 chr22 51304566 747128 0.014562602478695562 0.13218147332609007 chrMT 16571 11513 0.694767968137107 0.898214489889639 chrX 155270560 6247188 0.04023420795287915 0.2298548562357304 chrY 59373566 164167 0.002764984673482472 0.06126566743636239