BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006161.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 5,428,862 number of mapped reads = 4,258,826 (78.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,141,764 number of mapped paired reads (second in pair) = 2,117,062 number of mapped paired reads (both in pair) = 3,963,970 number of mapped paired reads (singletons) = 294,856 number of mapped bases = 164,332,978 bp number of sequenced bases = 164,313,144 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 214,154 duplication rate = 4.46% >>>>>>> Insert size mean insert size = 50,363.375 std insert size = 2,116,083.0297 median insert size = 73 >>>>>>> Mapping quality mean mapping quality = 46.4512 >>>>>>> ACTG content number of A's = 43,459,864 bp (26.45%) number of C's = 37,858,023 bp (23.04%) number of T's = 44,187,002 bp (26.89%) number of G's = 38,785,461 bp (23.6%) number of N's = 22,794 bp (0.01%) GC percentage = 46.64% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 623,651 number of insertions = 5,675 mapped reads with insertion percentage = 0.13% number of deletions = 14,901 mapped reads with deletion percentage = 0.35% homopolymer indels = 37.77% >>>>>>> Coverage mean coverageData = 0.0531X std coverageData = 0.4164X There is a 4.01% of reference with a coverageData >= 1X There is a 0.99% of reference with a coverageData >= 2X There is a 0.16% of reference with a coverageData >= 3X There is a 0.06% of reference with a coverageData >= 4X There is a 0.02% 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 13989306 0.05612546096725673 0.4122205484200107 chr2 243199373 13920852 0.05724049296788278 0.3343687278024375 chr3 198022430 10787976 0.05447855578784686 0.2895794838262133 chr4 191154276 9888682 0.05173141928564549 0.31272841502506493 chr5 180915260 9550879 0.05279200328374732 0.28914517024655856 chr6 171115067 9125668 0.05333059303304951 0.30154709740864455 chr7 159138663 8750531 0.05498683245818146 0.35933892547214963 chr8 146364022 7826822 0.05347504047135299 0.5414846712617774 chr9 141213431 6569474 0.04652159467749212 0.29412335243693033 chr10 135534747 7793984 0.05750543069224898 0.366618131009075 chr11 135006516 7774263 0.05758435392851705 0.3228640615744256 chr12 133851895 7391593 0.055222176720023275 0.298018860585307 chr13 115169878 4659052 0.04045373739129948 0.25303250739303546 chr14 107349540 5325733 0.04961113946086774 1.3251752064382065 chr15 102531392 4917737 0.0479632325678364 0.2768517091288449 chr16 90354753 5333974 0.05903368470278481 0.3264440676908481 chr17 81195210 5242149 0.06456229376092507 0.32856902759620993 chr18 78077248 4161445 0.05329907375833738 0.3801427665414966 chr19 59128983 3993510 0.0675389597010319 0.3987445307196658 chr20 63025520 3833670 0.06082726489206277 0.3284586474946191 chr21 48129895 2139935 0.04446165943225099 0.31419199499191275 chr22 51304566 2505354 0.04883296352219411 0.4496956826415979 chrMT 16571 3107 0.1874962283507332 0.5328194057376912 chrX 155270560 8382992 0.05398957793415571 0.2972291395208875 chrY 59373566 464290 0.007819809913388055 0.20829144598811086