BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818929.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 2,990,213 number of mapped reads = 2,951,426 (98.7%) number of supplementary alignments = 40,079 (1.34%) number of secondary alignments = 0 number of mapped bases = 273,586,835 bp number of sequenced bases = 273,431,767 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,598,518 duplication rate = 45.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2322 >>>>>>> ACTG content number of A's = 78,914,725 bp (28.86%) number of C's = 56,794,174 bp (20.77%) number of T's = 79,250,959 bp (28.98%) number of G's = 58,460,314 bp (21.38%) number of N's = 11,595 bp (0%) GC percentage = 42.15% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 1,686,449 number of insertions = 36,709 mapped reads with insertion percentage = 1.21% number of deletions = 84,645 mapped reads with deletion percentage = 2.81% homopolymer indels = 43.21% >>>>>>> Coverage mean coverageData = 0.0884X std coverageData = 0.9158X There is a 3.23% of reference with a coverageData >= 1X There is a 1.87% of reference with a coverageData >= 2X There is a 1.2% of reference with a coverageData >= 3X There is a 0.78% of reference with a coverageData >= 4X There is a 0.52% of reference with a coverageData >= 5X There is a 0.34% of reference with a coverageData >= 6X There is a 0.23% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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 29025598 0.11645145710589824 1.360088558573416 chr2 243199373 25919114 0.1065755790414805 1.3831308889558784 chr3 198022430 18834122 0.09511105383364905 0.6648244539997994 chr4 191154276 22703600 0.11877108100893333 0.789334932878898 chr5 180915260 14101920 0.07794765350363479 0.6182928058267115 chr6 171115067 13067854 0.07636880976705576 0.6307610646887036 chr7 159138663 14095997 0.08857682183744374 0.8163962017365705 chr8 146364022 16655717 0.11379652439449908 0.8351929334701348 chr9 141213431 10207265 0.07228253663775083 1.0225694568721349 chr10 135534747 14124227 0.1042111142170797 1.0729447682895652 chr11 135006516 10687863 0.0791655344990904 0.6976234383205328 chr12 133851895 11552871 0.08631085125840018 0.6400169743008021 chr13 115169878 3960213 0.03438584001973155 0.39251699457989964 chr14 107349540 5335679 0.049703790067474905 0.5365635991587135 chr15 102531392 7795490 0.07603027568376328 0.5943846873036189 chr16 90354753 7777716 0.08607976605281628 1.0192327802707797 chr17 81195210 5711052 0.07033730191719438 0.6398577269545823 chr18 78077248 6975051 0.08933525679593625 1.2477215428946729 chr19 59128983 4077105 0.06895273338288264 1.1470313600594992 chr20 63025520 5916806 0.09387952689640641 0.7003920229145639 chr21 48129895 3612103 0.07504905215355238 0.6591872367224509 chr22 51304566 3095970 0.06034492134676668 0.5517053027351807 chrMT 16571 906446 54.7007422605757 35.24796109346942 chrX 155270560 16625016 0.10707126965987629 0.8417125228725104 chrY 59373566 822040 0.013845218594416243 0.7496745111709954