BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549090.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 = 10,279,026 number of mapped reads = 8,892,905 (86.52%) number of secondary alignments = 0 number of mapped bases = 353,118,672 bp number of sequenced bases = 353,087,198 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 354,124 duplication rate = 2.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.8154 >>>>>>> ACTG content number of A's = 105,508,281 bp (29.88%) number of C's = 70,918,633 bp (20.09%) number of T's = 107,021,540 bp (30.31%) number of G's = 69,551,591 bp (19.7%) number of N's = 87,153 bp (0.02%) GC percentage = 39.78% >>>>>>> Mismatches and indels general error rate = 0.0041 number of mismatches = 1,426,740 number of insertions = 8,418 mapped reads with insertion percentage = 0.09% number of deletions = 25,306 mapped reads with deletion percentage = 0.28% homopolymer indels = 45.64% >>>>>>> Coverage mean coverageData = 0.1141X std coverageData = 0.9401X There is a 9.36% of reference with a coverageData >= 1X There is a 1.48% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.06% 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 28087330 0.11268710138940838 2.3670514033136927 chr2 243199373 31687118 0.13029276189786887 0.7056846000472063 chr3 198022430 25529980 0.12892468797600354 0.43167797855466644 chr4 191154276 25451721 0.13314753680948263 0.4401327856974279 chr5 180915260 23279203 0.12867462368846055 0.43556700947113985 chr6 171115067 21430179 0.12523841047848813 0.516053841014641 chr7 159138663 20019866 0.12580139623266787 1.0208522456127698 chr8 146364022 18868922 0.1289177609508435 0.7793108560070131 chr9 141213431 14700456 0.10410097606083943 0.6720109789864995 chr10 135534747 17185771 0.12679974235684374 0.9470750123926048 chr11 135006516 16268084 0.12049850986451646 0.7212701810793655 chr12 133851895 16229886 0.1212525679968894 0.44519796995022737 chr13 115169878 12509723 0.10861974690986474 0.3743237360977759 chr14 107349540 10887865 0.10142442156715344 0.4903775417624961 chr15 102531392 9728942 0.09488744676362143 0.3548515549052626 chr16 90354753 9251478 0.10239060694460644 0.5375055719609316 chr17 81195210 7690919 0.09472133885730451 0.48823230232028786 chr18 78077248 10004721 0.12813875048464823 1.4313263180931532 chr19 59128983 5252278 0.08882747061622893 1.8336253017029824 chr20 63025520 6666670 0.10577731052437171 0.4028940382983571 chr21 48129895 4492644 0.09334414712519111 0.453103242462522 chr22 51304566 3005051 0.058572778882877596 0.3485111703057717 chrMT 16571 51497 3.1076579566712934 3.8664911375251547 chrX 155270560 11928763 0.07682565838623884 0.45105997068264425 chrY 59373566 2909605 0.049005057233719125 0.390144945039181