BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549061.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,659,987 number of mapped reads = 7,449,714 (86.02%) number of secondary alignments = 0 number of mapped bases = 296,188,206 bp number of sequenced bases = 296,159,433 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 312,836 duplication rate = 2.97% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7356 >>>>>>> ACTG content number of A's = 86,800,869 bp (29.31%) number of C's = 61,259,191 bp (20.68%) number of T's = 86,858,270 bp (29.33%) number of G's = 61,235,660 bp (20.68%) number of N's = 5,443 bp (0%) GC percentage = 41.36% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 897,627 number of insertions = 6,873 mapped reads with insertion percentage = 0.09% number of deletions = 22,844 mapped reads with deletion percentage = 0.31% homopolymer indels = 45.19% >>>>>>> Coverage mean coverageData = 0.0957X std coverageData = 1.0183X There is a 7.55% of reference with a coverageData >= 1X There is a 1.44% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.07% 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 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% 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 24420482 0.09797561146297004 1.9255993617999099 chr2 243199373 25240639 0.10378578977668663 0.5504843737720571 chr3 198022430 20047346 0.10123775372315147 0.38582213403901955 chr4 191154276 19311052 0.10102338490194172 0.4513272904080444 chr5 180915260 19266730 0.10649588099975646 0.4050073988485012 chr6 171115067 18179735 0.10624274833729282 0.43745391035167336 chr7 159138663 17126819 0.10762198624227476 0.7541248899786517 chr8 146364022 15883498 0.10852050786087308 3.2235704216621532 chr9 141213431 12421701 0.08796401951312974 0.48088358136966075 chr10 135534747 14221035 0.10492538123821488 0.645290478770874 chr11 135006516 13744620 0.10180708611131035 0.5295054938853094 chr12 133851895 13474395 0.10066644928710199 0.39723053456429264 chr13 115169878 9591208 0.08327878926814528 0.3422617335374197 chr14 107349540 9111050 0.08487274374906498 0.3889426275680484 chr15 102531392 8588380 0.08376341949985425 0.3427180423610775 chr16 90354753 8200040 0.09075383117919651 0.4116335788874697 chr17 81195210 7825871 0.09638340734632006 0.41290114224297925 chr18 78077248 7808435 0.10000909611978127 0.974940142954147 chr19 59128983 5627103 0.09516657846119221 1.3336134907910273 chr20 63025520 6379452 0.1012201406668283 0.4030045853095891 chr21 48129895 3863853 0.0802796889542352 0.4346253651999047 chr22 51304566 3469570 0.06762692427804574 0.3253663262550411 chrMT 16571 4253 0.25665318930662 0.577680845549995 chrX 155270560 9351486 0.0602270385319664 0.3587185054742177 chrY 59373566 3029453 0.05102359861625963 0.6634075038849957