BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006050.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 5,978,850 number of mapped reads = 5,183,570 (86.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,651,420 number of mapped paired reads (second in pair) = 2,532,150 number of mapped paired reads (both in pair) = 4,751,442 number of mapped paired reads (singletons) = 432,128 number of mapped bases = 200,310,414 bp number of sequenced bases = 200,290,256 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 208,039 duplication rate = 3.58% >>>>>>> Insert size mean insert size = 55,388.9155 std insert size = 2,332,846.8506 median insert size = 90 >>>>>>> Mapping quality mean mapping quality = 46.7692 >>>>>>> ACTG content number of A's = 54,368,011 bp (27.14%) number of C's = 44,438,128 bp (22.19%) number of T's = 55,636,275 bp (27.78%) number of G's = 45,768,047 bp (22.85%) number of N's = 79,795 bp (0.04%) GC percentage = 45.04% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,116,804 number of insertions = 6,152 mapped reads with insertion percentage = 0.12% number of deletions = 15,692 mapped reads with deletion percentage = 0.3% homopolymer indels = 44.76% >>>>>>> Coverage mean coverageData = 0.0647X std coverageData = 0.3839X There is a 4.51% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% 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 17085818 0.06854874796881649 0.40386688358402817 chr2 243199373 17432835 0.07168124977032733 0.428775720648838 chr3 198022430 13814256 0.06976106696599976 0.3530295248447585 chr4 191154276 12387936 0.0648059580942882 0.3534018302303606 chr5 180915260 12336678 0.06819036713652568 0.35101141059547064 chr6 171115067 11619108 0.06790230810008098 0.3812316848432741 chr7 159138663 10990697 0.06906365048448346 0.46289051167556133 chr8 146364022 10140804 0.06928481372286968 0.4113699600527183 chr9 141213431 8485669 0.060091090060689765 0.3595876284130625 chr10 135534747 9576139 0.07065449423091483 0.37630100589764176 chr11 135006516 9389408 0.06954781352923736 0.5203743255148131 chr12 133851895 9356390 0.06990106490460968 0.3564531035426257 chr13 115169878 6284133 0.054564032793366336 0.3148432669933563 chr14 107349540 6193395 0.05769372649384431 0.33161706575466526 chr15 102531392 6138506 0.05986952756868843 0.332323057135736 chr16 90354753 6250995 0.06918280214877019 0.393529916020794 chr17 81195210 6008747 0.07400371278059382 0.4016800142619025 chr18 78077248 5217896 0.06682991695608943 0.4567610390299342 chr19 59128983 4342259 0.07343706554195258 0.4483229145033728 chr20 63025520 4601078 0.0730034119512223 0.36950895243336496 chr21 48129895 2669384 0.05546207819485166 0.3496705772345878 chr22 51304566 2702949 0.05268437511000483 0.3386819984537099 chrMT 16571 3999 0.24132520668637983 0.6634242572815915 chrX 155270560 5986996 0.03855847496138354 0.2751064711219984 chrY 59373566 1294339 0.02179992018670396 0.22837361547483429