BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819109.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 = 1,380,560 number of mapped reads = 1,263,504 (91.52%) number of supplementary alignments = 4,504 (0.33%) number of secondary alignments = 0 number of mapped bases = 73,285,087 bp number of sequenced bases = 73,262,156 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,454 duplication rate = 2.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8472 >>>>>>> ACTG content number of A's = 18,013,602 bp (24.59%) number of C's = 13,701,420 bp (18.7%) number of T's = 23,541,269 bp (32.13%) number of G's = 18,004,805 bp (24.58%) number of N's = 1,060 bp (0%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 368,801 number of insertions = 4,420 mapped reads with insertion percentage = 0.35% number of deletions = 13,751 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.06% >>>>>>> Coverage mean coverageData = 0.0237X std coverageData = 0.2325X There is a 2.15% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% 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 7351539 0.02949456643480138 0.417143157716082 chr2 243199373 5715254 0.02350028262613983 0.2573649844697404 chr3 198022430 3981070 0.020104136687949945 0.15410599000869998 chr4 191154276 4167694 0.021802776726794225 0.1772739892940226 chr5 180915260 3993973 0.02207648486921446 0.1606843059114664 chr6 171115067 3273902 0.019132751179649188 0.18164805887081617 chr7 159138663 3691609 0.023197436313763677 0.303237835680686 chr8 146364022 6010304 0.0410640806249503 0.24896617022773596 chr9 141213431 3111826 0.022036331657432785 0.20148081562680012 chr10 135534747 3924275 0.028954014279452635 0.24403310989425173 chr11 135006516 2604254 0.01928983931412614 0.21737541911276206 chr12 133851895 3496549 0.026122521462994604 0.1748851619821259 chr13 115169878 1706707 0.014819039749264995 0.13180166557903145 chr14 107349540 1746754 0.016271648672178753 0.14111895172792482 chr15 102531392 1976823 0.019280173237090158 0.15274885182762923 chr16 90354753 2295889 0.025409720283336948 0.18600877424950021 chr17 81195210 2607456 0.032113421469074345 0.2056218373657731 chr18 78077248 1697313 0.02173889376838692 0.3379845442199174 chr19 59128983 1538861 0.0260254941303489 0.29250057366039794 chr20 63025520 2150273 0.034117497166227265 0.20057464232645808 chr21 48129895 1008494 0.02095358820126244 0.1677767931132837 chr22 51304566 623229 0.012147632239984253 0.11928676628281176 chrMT 16571 48892 2.9504556152314283 2.369093132976443 chrX 155270560 4312881 0.02777655339170542 0.19656870644945512 chrY 59373566 249266 0.004198265605269523 0.120331088033339