BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004051.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,595,605 number of mapped reads = 1,705,921 (65.72%) number of supplementary alignments = 13,362 (0.51%) number of secondary alignments = 0 number of mapped bases = 109,194,218 bp number of sequenced bases = 109,145,455 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,424 duplication rate = 1.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0944 >>>>>>> ACTG content number of A's = 30,589,784 bp (28.03%) number of C's = 20,926,142 bp (19.17%) number of T's = 32,785,997 bp (30.04%) number of G's = 24,831,011 bp (22.75%) number of N's = 12,521 bp (0.01%) GC percentage = 41.92% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 846,524 number of insertions = 8,579 mapped reads with insertion percentage = 0.5% number of deletions = 28,228 mapped reads with deletion percentage = 1.63% homopolymer indels = 43.99% >>>>>>> Coverage mean coverageData = 0.0353X std coverageData = 0.3311X There is a 3.16% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9727762 0.039028035159840185 0.5753763210568184 chr2 243199373 8796452 0.036169714960572696 0.3982937655190249 chr3 198022430 8169854 0.04125721515486907 0.2235769978802964 chr4 191154276 7111066 0.037200664033275405 0.22839842822739537 chr5 180915260 6559556 0.036257615858385855 0.21847331805297696 chr6 171115067 5910216 0.03453942486549124 0.2248316343146521 chr7 159138663 6889297 0.04329115797585908 0.510564138771677 chr8 146364022 6843657 0.04675778177235387 0.35581197403675746 chr9 141213431 4007598 0.028379722605847597 0.3014102127161533 chr10 135534747 4632973 0.03418291694601385 0.26896694517236763 chr11 135006516 4178662 0.030951557923322753 0.29277759371762474 chr12 133851895 4708432 0.03517643138335845 0.21200466326935574 chr13 115169878 3007069 0.02610985660677699 0.1778676196772743 chr14 107349540 2784697 0.025940465138462633 0.2032493370979503 chr15 102531392 3015676 0.02941222138094058 0.2183513824531907 chr16 90354753 2785389 0.03082725487612146 0.2115447612350062 chr17 81195210 2916216 0.03591610884435178 0.2265102883286435 chr18 78077248 2974260 0.038093811913042834 0.5251047408158692 chr19 59128983 2038944 0.034482987809886734 0.38149397701322196 chr20 63025520 2123514 0.03369292312066604 0.23936297215557314 chr21 48129895 1216091 0.02526685337667992 0.191579201245256 chr22 51304566 1071554 0.020886133214731803 0.17398153545131503 chrMT 16571 340369 20.54003982861626 14.129792841007388 chrX 155270560 7115818 0.04582850734872084 0.27404200953426455 chrY 59373566 269096 0.0045322526189516725 0.09019119575543018