BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080815.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 = 2,883,665 number of mapped reads = 2,684,624 (93.1%) number of supplementary alignments = 21,260 (0.74%) number of secondary alignments = 0 number of mapped bases = 186,376,998 bp number of sequenced bases = 186,308,859 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 155,738 duplication rate = 4.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.4942 >>>>>>> ACTG content number of A's = 53,956,595 bp (28.96%) number of C's = 35,164,218 bp (18.87%) number of T's = 58,316,482 bp (31.3%) number of G's = 38,845,200 bp (20.85%) number of N's = 26,364 bp (0.01%) GC percentage = 39.72% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,472,089 number of insertions = 13,481 mapped reads with insertion percentage = 0.5% number of deletions = 38,530 mapped reads with deletion percentage = 1.42% homopolymer indels = 48.6% >>>>>>> Coverage mean coverageData = 0.0602X std coverageData = 0.4031X There is a 4.28% of reference with a coverageData >= 1X There is a 1.18% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% 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 14693697 0.05895149605264173 0.5034566026158249 chr2 243199373 15599398 0.0641424268803522 0.4579660558233487 chr3 198022430 12751660 0.06439502838138084 0.33682025740576993 chr4 191154276 13218385 0.06915034953233272 0.3555836610920831 chr5 180915260 12099115 0.06687724960293565 0.3430061913204299 chr6 171115067 11293743 0.0660008682929131 0.4165584788458208 chr7 159138663 10439284 0.06559866598854107 0.43631497792956225 chr8 146364022 9772595 0.06676910668661455 0.6131796023962829 chr9 141213431 7587964 0.05373401061263075 0.3703310735336974 chr10 135534747 8846350 0.06526997833256737 0.45923093036769885 chr11 135006516 7910994 0.05859712726754611 0.36532220894309025 chr12 133851895 8386170 0.06265260570274332 0.3339307842709254 chr13 115169878 6254443 0.054306239692291765 0.30942334454483617 chr14 107349540 5373796 0.05005886378274187 0.31133629662816403 chr15 102531392 4910783 0.04789540943714097 0.28912201848732905 chr16 90354753 4739181 0.05245082126448843 0.3202690383183566 chr17 81195210 4662868 0.057427870437184655 0.3298045191962383 chr18 78077248 5141612 0.06585288456888234 0.6078931051075028 chr19 59128983 3091196 0.05227886297317172 0.4205528291185156 chr20 63025520 3861739 0.06127262416874942 0.3338176372515769 chr21 48129895 2425263 0.0503899499469093 0.3125138045586091 chr22 51304566 1872989 0.03650725746320513 0.2512454170461396 chrMT 16571 18745 1.1311930480960715 1.4068197867452774 chrX 155270560 11013561 0.07093141803571779 0.36609719733786633 chrY 59373566 411467 0.0069301379000884 0.15099881226696563