BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819096.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 = 3,825,254 number of mapped reads = 3,506,543 (91.67%) number of supplementary alignments = 14,670 (0.38%) number of secondary alignments = 0 number of mapped bases = 207,301,162 bp number of sequenced bases = 207,239,897 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 503,079 duplication rate = 9.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4825 >>>>>>> ACTG content number of A's = 53,618,060 bp (25.87%) number of C's = 36,018,903 bp (17.38%) number of T's = 65,852,925 bp (31.78%) number of G's = 51,747,057 bp (24.97%) number of N's = 2,952 bp (0%) GC percentage = 42.35% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,029,376 number of insertions = 15,449 mapped reads with insertion percentage = 0.44% number of deletions = 37,004 mapped reads with deletion percentage = 1.05% homopolymer indels = 43.12% >>>>>>> Coverage mean coverageData = 0.067X std coverageData = 0.6067X There is a 4.38% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.49% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 20082896 0.08057310316590946 1.13217433670162 chr2 243199373 16117581 0.06627311905117453 0.6973026789314125 chr3 198022430 10879023 0.05493833703586003 0.3354506883985323 chr4 191154276 11273996 0.05897851848210814 0.5079801530446425 chr5 180915260 12257174 0.06775091277540657 0.3769036795084994 chr6 171115067 8741019 0.051082696300495854 0.39396165285885726 chr7 159138663 10008162 0.06288956945679505 0.6578758796833768 chr8 146364022 21200834 0.14485003698518206 0.8847450074634523 chr9 141213431 8733373 0.06184520082937437 0.4778521837859278 chr10 135534747 10532789 0.07771283182459476 0.7291890399901967 chr11 135006516 7031882 0.05208550082130851 0.49901508713447973 chr12 133851895 9303111 0.06950302048394608 0.3839241890632565 chr13 115169878 4556359 0.03956207195079255 0.2871997294832156 chr14 107349540 4893881 0.045588281048991916 0.31340010895030057 chr15 102531392 5412438 0.052788106105103885 0.32618775370854475 chr16 90354753 6443702 0.0713155842504489 0.429593523947736 chr17 81195210 7133727 0.08785896360142427 0.46649730935520745 chr18 78077248 4818096 0.061709347132726806 0.913508509807683 chr19 59128983 4250136 0.07187906478959734 0.7236016327864868 chr20 63025520 5984249 0.09494961723441551 0.46752920909832096 chr21 48129895 2878747 0.05981203574202686 0.4786146243505237 chr22 51304566 1636992 0.031907335499144464 0.2551894098691481 chrMT 16571 118175 7.131434433649146 5.680054927665432 chrX 155270560 12185281 0.07847772945495914 0.4430194431579478 chrY 59373566 827539 0.0139378355681045 0.481576894406222