BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708645.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,508,376 number of mapped reads = 3,385,028 (96.48%) number of supplementary alignments = 107 (0%) number of secondary alignments = 0 number of mapped bases = 168,846,298 bp number of sequenced bases = 168,829,641 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,184 duplication rate = 0.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6546 >>>>>>> ACTG content number of A's = 52,186,603 bp (30.91%) number of C's = 32,063,363 bp (18.99%) number of T's = 52,180,121 bp (30.91%) number of G's = 32,395,010 bp (19.19%) number of N's = 4,544 bp (0%) GC percentage = 38.18% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 272,851 number of insertions = 11,556 mapped reads with insertion percentage = 0.34% number of deletions = 9,780 mapped reads with deletion percentage = 0.29% homopolymer indels = 49.12% >>>>>>> Coverage mean coverageData = 0.0545X std coverageData = 0.2402X There is a 5.17% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 12485714 0.05009301060076396 0.2306190516788995 chr2 243199373 14205812 0.058412206515022554 0.24788866601656165 chr3 198022430 13522120 0.06828579974500869 0.2677227722043295 chr4 191154276 12983426 0.06792119052570919 0.2665103035218725 chr5 180915260 12390930 0.06849024233776631 0.2681430334583632 chr6 171115067 10643837 0.0622028041516648 0.2552760049891376 chr7 159138663 9344717 0.05872059513281194 0.24907729679070548 chr8 146364022 9123595 0.06233495687895212 0.25576712635948007 chr9 141213431 6883392 0.04874459852193521 0.22724930450659456 chr10 135534747 7871610 0.05807816943060365 0.24714517039707884 chr11 135006516 8205968 0.06078201440291963 0.25476719669441583 chr12 133851895 7521139 0.05619000761998924 0.2432103783988757 chr13 115169878 6605314 0.05735279149987465 0.24577339416479282 chr14 107349540 5377235 0.0500908993182458 0.23054163998040667 chr15 102531392 4222567 0.04118316271371796 0.2091625026710493 chr16 90354753 3310519 0.03663912400933684 0.19626799499212216 chr17 81195210 2824844 0.03479077152457639 0.19171511126851065 chr18 78077248 7576353 0.09703662967219337 0.32115233593936304 chr19 59128983 1350592 0.02284145492575105 0.15417250424036644 chr20 63025520 2569152 0.04076367795140762 0.20645007541014251 chr21 48129895 1949312 0.04050106487869961 0.20817157902481728 chr22 51304566 996033 0.01941411998300502 0.14306516019274418 chrMT 16571 800 0.048277110614929696 0.21659172056637377 chrX 155270560 6096133 0.03926135772293215 0.20212293989998528 chrY 59373566 785184 0.013224470970802057 0.11815933203735689