BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080691.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 = 2,605,805 number of mapped reads = 2,311,597 (88.71%) number of supplementary alignments = 22,611 (0.87%) number of secondary alignments = 0 number of mapped bases = 160,310,080 bp number of sequenced bases = 160,249,840 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 148,769 duplication rate = 5.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.6209 >>>>>>> ACTG content number of A's = 47,241,905 bp (29.48%) number of C's = 29,344,306 bp (18.31%) number of T's = 50,851,771 bp (31.73%) number of G's = 32,809,544 bp (20.47%) number of N's = 2,314 bp (0%) GC percentage = 38.79% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,295,680 number of insertions = 12,392 mapped reads with insertion percentage = 0.53% number of deletions = 34,128 mapped reads with deletion percentage = 1.46% homopolymer indels = 48.18% >>>>>>> Coverage mean coverageData = 0.0518X std coverageData = 0.4846X There is a 3.61% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.32% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 12119663 0.048624404430270204 0.5824045717228459 chr2 243199373 13537945 0.05566603578373535 0.4155201221514553 chr3 198022430 11053097 0.05581739906938825 0.3174584294773219 chr4 191154276 11558723 0.060468032637679525 0.3471816628272509 chr5 180915260 10400597 0.05748877678975228 0.322792116447474 chr6 171115067 9493951 0.05548284652221771 0.3374733652772383 chr7 159138663 8566799 0.053832292156432156 0.53468557737805 chr8 146364022 8377658 0.05723850633183611 1.399431712071681 chr9 141213431 6499496 0.04602604691334212 0.35716843179003605 chr10 135534747 7452598 0.05498662272929908 0.3847823280708822 chr11 135006516 7466731 0.0553064490605772 0.4152560488576113 chr12 133851895 7017484 0.05242722936421632 0.3087561747387646 chr13 115169878 5587598 0.048516140652680034 0.2980316604191842 chr14 107349540 5121694 0.047710441982331736 0.3020369010692846 chr15 102531392 4471935 0.04361527638286623 0.2788155219712265 chr16 90354753 3888628 0.04303733750453615 0.2912821154236243 chr17 81195210 3657019 0.0450398367095793 0.30931200582665225 chr18 78077248 4524708 0.057951683952795055 0.5385347227556954 chr19 59128983 2525956 0.04271942238546535 0.44695793004354906 chr20 63025520 2970782 0.04713617594904413 0.2952059631293298 chr21 48129895 1961898 0.040762565553072574 0.28494356293480627 chr22 51304566 1431619 0.027904319471292283 0.21714525526109793 chrMT 16571 73056 4.40866574135538 3.7300546324021453 chrX 155270560 10130937 0.06524699208916358 0.35955500857053285 chrY 59373566 419508 0.007065568539373229 0.19393511868764363