BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818960.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 = 454,210 number of mapped reads = 422,492 (93.02%) number of supplementary alignments = 6,271 (1.38%) number of secondary alignments = 0 number of mapped bases = 38,966,032 bp number of sequenced bases = 38,943,875 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,371 duplication rate = 13.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1462 >>>>>>> ACTG content number of A's = 11,360,933 bp (29.17%) number of C's = 8,491,519 bp (21.8%) number of T's = 11,224,291 bp (28.82%) number of G's = 7,865,294 bp (20.2%) number of N's = 1,838 bp (0%) GC percentage = 42% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 278,813 number of insertions = 5,268 mapped reads with insertion percentage = 1.21% number of deletions = 12,234 mapped reads with deletion percentage = 2.83% homopolymer indels = 43.04% >>>>>>> Coverage mean coverageData = 0.0126X std coverageData = 0.1839X There is a 0.99% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.04% 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 4566938 0.018322674510006538 0.30643614360787247 chr2 243199373 3362374 0.013825586630932639 0.2376645433406745 chr3 198022430 2539350 0.012823547312291845 0.13754373257879518 chr4 191154276 2638917 0.013805168554011316 0.15059228150756548 chr5 180915260 2050840 0.011335914947141552 0.13221881226386256 chr6 171115067 2052162 0.011992877284149385 0.14169571708729548 chr7 159138663 1963903 0.012340828828001402 0.164333645760287 chr8 146364022 2593291 0.017718090583763817 0.17832600631939186 chr9 141213431 1468603 0.010399881863928368 0.1960712010113567 chr10 135534747 1929036 0.01423277825574869 0.2214744511142923 chr11 135006516 1481471 0.010973329613216594 0.14427731934094906 chr12 133851895 1705173 0.012739251842493526 0.13897308442075362 chr13 115169878 628524 0.00545736446816415 0.08786303106392558 chr14 107349540 967650 0.009014011611041836 0.12334513194283193 chr15 102531392 1135643 0.011076051713020731 0.12806445304703418 chr16 90354753 1155547 0.012789000707024234 0.18236831932947184 chr17 81195210 828052 0.010198286327481633 0.13087686270369067 chr18 78077248 982886 0.012588635296162078 0.22554984597551048 chr19 59128983 590596 0.009988265822194168 0.27236581016620964 chr20 63025520 817867 0.012976759255615821 0.14460315684040165 chr21 48129895 515633 0.010713362246063491 0.136004785397848 chr22 51304566 464057 0.00904514034871672 0.11991565320896173 chrMT 16571 103865 6.267877617524591 4.982457128969363 chrX 155270560 2290807 0.014753646795632088 0.16740115476081632 chrY 59373566 132847 0.002237477196501891 0.1396502955399864