BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004016.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,585,084 number of mapped reads = 2,256,828 (87.3%) number of supplementary alignments = 18,839 (0.73%) number of secondary alignments = 0 number of mapped bases = 148,667,560 bp number of sequenced bases = 148,607,113 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 115,451 duplication rate = 4.27% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4658 >>>>>>> ACTG content number of A's = 40,812,965 bp (27.46%) number of C's = 28,080,680 bp (18.9%) number of T's = 46,386,874 bp (31.21%) number of G's = 33,301,585 bp (22.41%) number of N's = 25,009 bp (0.02%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,297,098 number of insertions = 10,319 mapped reads with insertion percentage = 0.45% number of deletions = 34,901 mapped reads with deletion percentage = 1.53% homopolymer indels = 46.51% >>>>>>> Coverage mean coverageData = 0.048X std coverageData = 0.3668X There is a 3.89% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 16631211 0.06672485281390733 0.6529003829051584 chr2 243199373 11487844 0.047236322439038525 0.4415471633420589 chr3 198022430 9196976 0.04644411241696206 0.25426655718885705 chr4 191154276 10796007 0.05647797802859508 0.2914772006389153 chr5 180915260 6644600 0.036727692290854846 0.22684797039595708 chr6 171115067 6142178 0.03589501560373991 0.24623954965722128 chr7 159138663 9010575 0.056620904248768256 0.4790523401311632 chr8 146364022 7900818 0.05398060187222786 0.45021907162274655 chr9 141213431 7494324 0.053070900883358606 0.3430161591637391 chr10 135534747 9155183 0.06754860434424244 0.37744921950435945 chr11 135006516 5079934 0.03762732459520694 0.27878044165861315 chr12 133851895 7266530 0.0542878380616128 0.28201821408077976 chr13 115169878 2891386 0.02510540125778374 0.20342476257668085 chr14 107349540 3361028 0.03130919797141189 0.22581285056773054 chr15 102531392 3584373 0.03495878608572875 0.22788250781182973 chr16 90354753 5528873 0.06119072673465224 0.306394808558168 chr17 81195210 4283997 0.05276169616409638 0.28284996683497793 chr18 78077248 4008012 0.05133393021229437 0.5393246362353497 chr19 59128983 2981936 0.05043103819323258 0.4625270230955383 chr20 63025520 2919629 0.04632455234006796 0.2639298843078473 chr21 48129895 2114738 0.043938138655818804 0.2616855027133723 chr22 51304566 912061 0.01777738457041036 0.15486587522611941 chrMT 16571 78864 4.75915756441977 4.0021574456824345 chrX 155270560 8888529 0.05724542373003614 0.303020081314608 chrY 59373566 307954 0.005186718951662765 0.10214531655354855