BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472425.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 = 14,795,582 number of mapped reads = 14,654,636 (99.05%) number of supplementary alignments = 56,629 (0.38%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,346,022 number of mapped paired reads (second in pair) = 7,308,614 number of mapped paired reads (both in pair) = 14,580,540 number of mapped paired reads (singletons) = 74,096 number of mapped bases = 1,435,989,496 bp number of sequenced bases = 1,435,821,584 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,934,307 duplication rate = 45.95% >>>>>>> Insert size mean insert size = 16,727.2609 std insert size = 1,280,256.6263 median insert size = 206 >>>>>>> Mapping quality mean mapping quality = 54.7795 >>>>>>> ACTG content number of A's = 387,881,094 bp (27.01%) number of C's = 331,251,312 bp (23.07%) number of T's = 388,381,778 bp (27.05%) number of G's = 328,131,352 bp (22.85%) number of N's = 176,048 bp (0.01%) GC percentage = 45.92% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 7,593,072 number of insertions = 87,993 mapped reads with insertion percentage = 0.59% number of deletions = 69,368 mapped reads with deletion percentage = 0.47% homopolymer indels = 46.62% >>>>>>> Coverage mean coverageData = 0.4639X std coverageData = 15.8831X There is a 4.29% of reference with a coverageData >= 1X There is a 1.9% of reference with a coverageData >= 2X There is a 0.8% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.45% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.38% of reference with a coverageData >= 7X There is a 0.36% of reference with a coverageData >= 8X There is a 0.34% of reference with a coverageData >= 9X There is a 0.33% of reference with a coverageData >= 10X There is a 0.32% of reference with a coverageData >= 11X There is a 0.31% of reference with a coverageData >= 12X There is a 0.3% of reference with a coverageData >= 13X There is a 0.29% of reference with a coverageData >= 14X There is a 0.28% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.27% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.25% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.24% of reference with a coverageData >= 21X There is a 0.24% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.22% of reference with a coverageData >= 26X There is a 0.22% of reference with a coverageData >= 27X There is a 0.21% of reference with a coverageData >= 28X There is a 0.21% of reference with a coverageData >= 29X There is a 0.21% of reference with a coverageData >= 30X There is a 0.2% of reference with a coverageData >= 31X There is a 0.2% of reference with a coverageData >= 32X There is a 0.2% of reference with a coverageData >= 33X There is a 0.19% of reference with a coverageData >= 34X There is a 0.19% of reference with a coverageData >= 35X There is a 0.19% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.18% of reference with a coverageData >= 38X There is a 0.18% of reference with a coverageData >= 39X There is a 0.18% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.17% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.16% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.16% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 143290576 0.5748855325820833 17.82480880646799 chr2 243199373 99663935 0.40980342083365484 13.63885283446106 chr3 198022430 111747571 0.5643177442070577 13.005715468848566 chr4 191154276 34234540 0.17909377031147344 5.949925443440739 chr5 180915260 69555950 0.384467015109726 15.787129453837716 chr6 171115067 85422844 0.49921287176891327 18.22204543322435 chr7 159138663 102411229 0.6435345570296767 16.478142714259466 chr8 146364022 100183029 0.6844785189081508 20.042930339045153 chr9 141213431 37387582 0.26475939105254087 7.361010521560168 chr10 135534747 37723339 0.2783296522477738 10.882092529337665 chr11 135006516 38623662 0.2860873915152362 8.283623001858006 chr12 133851895 69746667 0.5210734371747221 13.380574923648137 chr13 115169878 59590952 0.5174178616391345 15.05853198829127 chr14 107349540 24344168 0.2267747770507447 6.618297217885794 chr15 102531392 32454512 0.3165324430589999 10.71581824219354 chr16 90354753 95948472 1.0619084089577446 35.81975928526503 chr17 81195210 62204735 0.7661133581648474 18.157493645730472 chr18 78077248 9202839 0.1178683833733484 4.315084469187434 chr19 59128983 34305764 0.580185253651327 13.793464225981792 chr20 63025520 74712198 1.1854277124567953 34.36627000526159 chr21 48129895 7710512 0.16020213632296518 10.500195141023527 chr22 51304566 22748153 0.44339431698925197 23.12139165938916 chrMT 16571 18760 1.1320982439201013 1.423424072294351 chrX 155270560 82499567 0.5313278125615055 17.961537030919363 chrY 59373566 257940 0.0043443575546734045 0.26598329476981053