BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081954.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 = 2,791,217 number of mapped reads = 2,597,853 (93.07%) number of supplementary alignments = 18,724 (0.67%) number of secondary alignments = 0 number of mapped bases = 177,868,556 bp number of sequenced bases = 177,805,767 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,822 duplication rate = 3.84% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9961 >>>>>>> ACTG content number of A's = 50,596,401 bp (28.46%) number of C's = 32,842,673 bp (18.47%) number of T's = 56,413,264 bp (31.73%) number of G's = 37,930,155 bp (21.33%) number of N's = 23,274 bp (0.01%) GC percentage = 39.8% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 1,288,930 number of insertions = 12,013 mapped reads with insertion percentage = 0.46% number of deletions = 35,412 mapped reads with deletion percentage = 1.35% homopolymer indels = 49.01% >>>>>>> Coverage mean coverageData = 0.0575X std coverageData = 0.432X There is a 4.8% of reference with a coverageData >= 1X There is a 0.71% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 16396538 0.06578333861001695 0.7155219910164126 chr2 243199373 15508135 0.06376716686683234 0.5575598852097612 chr3 198022430 11389105 0.057514216950069745 0.2760493199720209 chr4 191154276 9324667 0.0487808444316464 0.2661263501638931 chr5 180915260 9048877 0.05001721247837247 0.25826764286130255 chr6 171115067 15651803 0.09146946130699292 0.445672382263527 chr7 159138663 11748980 0.07382857049641042 0.5283710883669576 chr8 146364022 10201615 0.06970029151016362 0.647431066510111 chr9 141213431 8709810 0.06167833993071098 0.45344887782101156 chr10 135534747 6994033 0.05160324680430473 0.41500053625989697 chr11 135006516 8044737 0.05958776834149249 0.3453920357924212 chr12 133851895 7671416 0.0573127186581856 0.2828696555392346 chr13 115169878 4871184 0.04229564261585829 0.2362788065984522 chr14 107349540 4418930 0.041163939780272926 0.25267843235302656 chr15 102531392 4050642 0.039506359184121875 0.22883542045100058 chr16 90354753 3759612 0.04160945467915783 0.2671238157521205 chr17 81195210 4660725 0.057401477254631156 0.30273555573306976 chr18 78077248 5067171 0.06489945700955034 0.6949688016877553 chr19 59128983 3530192 0.059703242316885445 0.5357382412389747 chr20 63025520 4462935 0.07081155379598614 0.3107499411077587 chr21 48129895 1949495 0.040504867089363066 0.2559452831304423 chr22 51304566 1434559 0.02796162431234678 0.19011000875353234 chrMT 16571 50423 3.04284593567075 2.312828359029613 chrX 155270560 8553308 0.0550864761484727 0.30619230392680086 chrY 59373566 369664 0.006226070369430059 0.1401283968296076