BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708564.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 = 4,085,212 number of mapped reads = 3,348,071 (81.96%) number of supplementary alignments = 103 (0%) number of secondary alignments = 0 number of mapped bases = 166,952,525 bp number of sequenced bases = 166,936,899 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,939 duplication rate = 0.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8059 >>>>>>> ACTG content number of A's = 51,732,660 bp (30.99%) number of C's = 31,693,586 bp (18.99%) number of T's = 51,547,364 bp (30.88%) number of G's = 31,957,761 bp (19.14%) number of N's = 5,528 bp (0%) GC percentage = 38.13% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 270,154 number of insertions = 11,286 mapped reads with insertion percentage = 0.34% number of deletions = 9,191 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.57% >>>>>>> Coverage mean coverageData = 0.0539X std coverageData = 0.2429X There is a 5.03% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.03% 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 12393996 0.04972503558978094 0.2341112337535689 chr2 243199373 10214487 0.04200046601271459 0.2127525979640119 chr3 198022430 10698753 0.054027985617588876 0.2415403368802963 chr4 191154276 9849753 0.051527767027298936 0.23578206247947153 chr5 180915260 9909442 0.05477394223129658 0.24334156036279236 chr6 171115067 11237461 0.06567195511778048 0.26750832633402544 chr7 159138663 11050098 0.06943691615657221 0.27466707366370224 chr8 146364022 8496960 0.0580536110165106 0.25008139345208563 chr9 141213431 10739197 0.07604940212804545 0.29068508136757765 chr10 135534747 5058089 0.03731950006886426 0.2001519616668425 chr11 135006516 10207546 0.07560780251525046 0.28851905659388927 chr12 133851895 8209282 0.06133108537611664 0.2580195778390169 chr13 115169878 8077093 0.07013199232528491 0.27644717233391636 chr14 107349540 5017210 0.04673713552941168 0.22655620343428415 chr15 102531392 6891054 0.06720921139937318 0.27332823309787474 chr16 90354753 2963283 0.03279609430175743 0.18787346734199611 chr17 81195210 2054568 0.02530405426625536 0.16404874881313855 chr18 78077248 4767219 0.06105772324352416 0.25661076187239956 chr19 59128983 592811 0.01002572630075508 0.10216769767425818 chr20 63025520 3901639 0.06190570105569934 0.2610677629878179 chr21 48129895 2648152 0.055020938649461004 0.247388036259941 chr22 51304566 857249 0.016709019622152148 0.13349280037574482 chrMT 16571 150 0.009051958240299317 0.09471019106894038 chrX 155270560 10832565 0.0697657366599309 0.2760684336149208 chrY 59373566 284468 0.004791155713975475 0.07293766228935057