BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081244.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 = 1,786,982 number of mapped reads = 1,598,142 (89.43%) number of supplementary alignments = 16,945 (0.95%) number of secondary alignments = 0 number of mapped bases = 103,211,175 bp number of sequenced bases = 103,170,431 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,190 duplication rate = 2.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3797 >>>>>>> ACTG content number of A's = 30,172,152 bp (29.24%) number of C's = 19,774,865 bp (19.17%) number of T's = 31,614,302 bp (30.64%) number of G's = 21,595,713 bp (20.93%) number of N's = 13,399 bp (0.01%) GC percentage = 40.1% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 955,489 number of insertions = 7,963 mapped reads with insertion percentage = 0.49% number of deletions = 24,894 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.99% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 0.2834X There is a 2.88% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 11631089 0.04666423278439896 0.4313487174990923 chr2 243199373 6533197 0.026863543764152713 0.28476473638663263 chr3 198022430 6873281 0.0347096084014321 0.21052680094699078 chr4 191154276 3711794 0.0194177921502525 0.16383874452158975 chr5 180915260 6104481 0.03374221168518344 0.2061866535198938 chr6 171115067 7661434 0.044773579172896566 0.2730863129818526 chr7 159138663 7398073 0.04648821889373295 0.4357728900614314 chr8 146364022 6959937 0.047552239306460166 0.44476690393594204 chr9 141213431 2966552 0.021007576821782625 0.2114838311771125 chr10 135534747 3071413 0.022661443415687346 0.240789576942355 chr11 135006516 5749220 0.04258475939042824 0.3464619332494257 chr12 133851895 2860175 0.02136820700222436 0.16562854607515357 chr13 115169878 2904966 0.025223314033553115 0.18025427426134838 chr14 107349540 3635715 0.033868007259276564 0.21148536151243666 chr15 102531392 1921645 0.018742016103711925 0.15856680772082332 chr16 90354753 3446278 0.038141634895510146 0.22435873795972383 chr17 81195210 1734330 0.0213600038721496 0.18774103041802706 chr18 78077248 2437269 0.03121612329368986 0.3449010911197907 chr19 59128983 2406856 0.0407051817549441 0.36901649148206095 chr20 63025520 2505616 0.03975557837523594 0.226265031042176 chr21 48129895 1664537 0.03458426410446148 0.21534724498108476 chr22 51304566 698275 0.013610387036506653 0.1277225727460182 chrMT 16571 40508 2.444511495986965 2.38976668830707 chrX 155270560 8027492 0.0517000260706215 0.274335382563177 chrY 59373566 267042 0.004497658099228872 0.09059274760633142