BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818764.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 = 294,237 number of mapped reads = 183,268 (62.29%) number of supplementary alignments = 1,229 (0.42%) number of secondary alignments = 0 number of mapped bases = 12,422,185 bp number of sequenced bases = 12,415,794 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,582 duplication rate = 7.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9901 >>>>>>> ACTG content number of A's = 3,555,220 bp (28.63%) number of C's = 2,690,603 bp (21.67%) number of T's = 3,577,102 bp (28.81%) number of G's = 2,592,117 bp (20.88%) number of N's = 752 bp (0.01%) GC percentage = 42.55% >>>>>>> Mismatches and indels general error rate = 0.0058 number of mismatches = 68,284 number of insertions = 1,947 mapped reads with insertion percentage = 1.04% number of deletions = 3,517 mapped reads with deletion percentage = 1.89% homopolymer indels = 37.72% >>>>>>> Coverage mean coverageData = 0.004X std coverageData = 0.0901X There is a 0.36% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% 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 1026237 0.004117289641577262 0.09337138519978067 chr2 243199373 1124802 0.004625020147564278 0.1645983890882136 chr3 198022430 825142 0.004166911798830062 0.07081680387042427 chr4 191154276 796470 0.004166634493700784 0.07822891470629462 chr5 180915260 760669 0.004204559637478894 0.0745168907428452 chr6 171115067 715464 0.004181186452739431 0.0752054978773238 chr7 159138663 688458 0.004326151715878121 0.07692113576723181 chr8 146364022 636410 0.004348131400761862 0.07400948488399477 chr9 141213431 546236 0.003868158971365833 0.07262642822184645 chr10 135534747 598711 0.004417398587832241 0.10470435451776124 chr11 135006516 572038 0.004237114007149107 0.0735438243721763 chr12 133851895 556257 0.004155764847408399 0.07682345845126992 chr13 115169878 386456 0.003355530167358517 0.0635486308517719 chr14 107349540 376138 0.0035038622429122658 0.06792589482850113 chr15 102531392 359429 0.003505550768295431 0.06532588865725578 chr16 90354753 389372 0.004309369314528478 0.11262088413061938 chr17 81195210 340984 0.004199558077379195 0.07214757445851731 chr18 78077248 329887 0.004225136111354745 0.08547532092703136 chr19 59128983 265630 0.004492382356720054 0.08883994216104261 chr20 63025520 279104 0.004428428357274958 0.07598824729807087 chr21 48129895 168821 0.003507612056913899 0.0662061613052093 chr22 51304566 147414 0.0028733115099346127 0.062492111737912276 chrMT 16571 4495 0.27125701526763624 0.5694588391827654 chrX 155270560 402092 0.002589621625632058 0.059540907894907694 chrY 59373566 125469 0.0021132131426972066 0.15287390682555754