BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472390.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 22,565,804 number of mapped reads = 22,391,043 (99.23%) number of supplementary alignments = 115,530 (0.51%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,231,655 number of mapped paired reads (second in pair) = 11,159,388 number of mapped paired reads (both in pair) = 22,281,832 number of mapped paired reads (singletons) = 109,211 number of mapped bases = 2,197,517,504 bp number of sequenced bases = 2,197,229,696 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 14,446,896 duplication rate = 48.22% >>>>>>> Insert size mean insert size = 23,073.3831 std insert size = 1,472,522.0641 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 54.8613 >>>>>>> ACTG content number of A's = 601,239,870 bp (27.36%) number of C's = 498,400,962 bp (22.68%) number of T's = 601,346,067 bp (27.37%) number of G's = 495,967,143 bp (22.57%) number of N's = 275,654 bp (0.01%) GC percentage = 45.26% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 12,064,546 number of insertions = 136,313 mapped reads with insertion percentage = 0.6% number of deletions = 117,832 mapped reads with deletion percentage = 0.52% homopolymer indels = 45.84% >>>>>>> Coverage mean coverageData = 0.7099X std coverageData = 21.5872X There is a 5.86% of reference with a coverageData >= 1X There is a 2.49% of reference with a coverageData >= 2X There is a 1.05% of reference with a coverageData >= 3X There is a 0.77% of reference with a coverageData >= 4X There is a 0.58% of reference with a coverageData >= 5X There is a 0.52% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.46% of reference with a coverageData >= 8X There is a 0.44% of reference with a coverageData >= 9X There is a 0.42% of reference with a coverageData >= 10X There is a 0.41% of reference with a coverageData >= 11X There is a 0.4% of reference with a coverageData >= 12X There is a 0.39% of reference with a coverageData >= 13X There is a 0.38% of reference with a coverageData >= 14X There is a 0.37% of reference with a coverageData >= 15X There is a 0.36% of reference with a coverageData >= 16X There is a 0.35% of reference with a coverageData >= 17X There is a 0.35% of reference with a coverageData >= 18X There is a 0.34% of reference with a coverageData >= 19X There is a 0.33% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.32% of reference with a coverageData >= 22X There is a 0.31% of reference with a coverageData >= 23X There is a 0.31% of reference with a coverageData >= 24X There is a 0.3% of reference with a coverageData >= 25X There is a 0.3% of reference with a coverageData >= 26X There is a 0.29% of reference with a coverageData >= 27X There is a 0.29% of reference with a coverageData >= 28X There is a 0.29% of reference with a coverageData >= 29X There is a 0.28% of reference with a coverageData >= 30X There is a 0.28% of reference with a coverageData >= 31X There is a 0.27% of reference with a coverageData >= 32X There is a 0.27% of reference with a coverageData >= 33X There is a 0.27% of reference with a coverageData >= 34X There is a 0.26% of reference with a coverageData >= 35X There is a 0.26% of reference with a coverageData >= 36X There is a 0.26% of reference with a coverageData >= 37X There is a 0.25% of reference with a coverageData >= 38X There is a 0.25% of reference with a coverageData >= 39X There is a 0.25% of reference with a coverageData >= 40X There is a 0.24% of reference with a coverageData >= 41X There is a 0.24% of reference with a coverageData >= 42X There is a 0.24% of reference with a coverageData >= 43X There is a 0.24% of reference with a coverageData >= 44X There is a 0.23% of reference with a coverageData >= 45X There is a 0.23% of reference with a coverageData >= 46X There is a 0.23% of reference with a coverageData >= 47X There is a 0.23% of reference with a coverageData >= 48X There is a 0.22% of reference with a coverageData >= 49X There is a 0.22% of reference with a coverageData >= 50X There is a 0.22% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 233243611 0.9357794578975192 25.129517124131784 chr2 243199373 231700780 0.9527194792562232 35.535198155107274 chr3 198022430 161114270 0.8136162655917312 19.728454666922815 chr4 191154276 44816389 0.23445140719739901 7.3937235076992796 chr5 180915260 92837883 0.5131567287358734 16.20480470239231 chr6 171115067 149800215 0.875435562901074 21.320130256291055 chr7 159138663 176047692 1.1062534313235999 30.04461203205287 chr8 146364022 105905637 0.7235769798673611 19.6318371264506 chr9 141213431 85319136 0.6041857024208979 14.525524303099413 chr10 135534747 42577611 0.31414535344209554 9.779913349750592 chr11 135006516 54467125 0.40344071244679774 9.753175277441972 chr12 133851895 105453579 0.7878377739814592 20.674609354849842 chr13 115169878 87890201 0.763135313905603 26.41729060714866 chr14 107349540 39208174 0.3652383978543364 10.388336656546828 chr15 102531392 32207978 0.31412796970512213 10.123683589837045 chr16 90354753 105975687 1.1728844745998033 27.627256669353763 chr17 81195210 88366223 1.0883181778826607 24.44199490317402 chr18 78077248 31500375 0.40345139982392825 11.358507870340478 chr19 59128983 42675419 0.7217343650236636 15.409398521518314 chr20 63025520 69802652 1.1075299656393156 23.993375457328632 chr21 48129895 18355614 0.3813765643993198 20.84453455466458 chr22 51304566 16500464 0.3216178458658046 8.96399872108154 chrMT 16571 33095 1.997163719751373 1.6604324819367287 chrX 155270560 181225810 1.1671614374289627 30.741268630619317 chrY 59373566 491884 0.008284562190520947 0.6419602066219423