BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006433.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 = 3,772,723 number of mapped reads = 3,040,739 (80.6%) number of supplementary alignments = 7,760 (0.21%) number of secondary alignments = 0 number of mapped bases = 168,500,416 bp number of sequenced bases = 168,449,315 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 543,548 duplication rate = 17.14% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.737 >>>>>>> ACTG content number of A's = 47,139,611 bp (27.98%) number of C's = 36,026,838 bp (21.39%) number of T's = 48,994,736 bp (29.09%) number of G's = 36,280,549 bp (21.54%) number of N's = 7,581 bp (0%) GC percentage = 42.93% >>>>>>> Mismatches and indels general error rate = 0.0044 number of mismatches = 715,337 number of insertions = 12,694 mapped reads with insertion percentage = 0.42% number of deletions = 31,780 mapped reads with deletion percentage = 1.04% homopolymer indels = 43.33% >>>>>>> Coverage mean coverageData = 0.0544X std coverageData = 0.6768X There is a 3.87% of reference with a coverageData >= 1X There is a 1.05% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 13433920 0.0538972378327595 0.5207542497879579 chr2 243199373 14022953 0.057660317241031704 0.3905881138492758 chr3 198022430 11170054 0.05640802408090841 0.3119205431509967 chr4 191154276 10743021 0.056200788309857114 0.32907539112665934 chr5 180915260 10222786 0.05650593543076466 0.3122178957910747 chr6 171115067 9672829 0.056528213263651414 0.40893372116440907 chr7 159138663 13115177 0.08241351757492144 0.5496568303435165 chr8 146364022 8554423 0.05844621432991231 0.963533787007109 chr9 141213431 6898925 0.04885459514116614 0.3633058005125944 chr10 135534747 7837755 0.05782838108665964 0.4186705933752074 chr11 135006516 7621211 0.0564506901281713 0.3555063672585895 chr12 133851895 7474664 0.05584279550169984 0.3138174765827699 chr13 115169878 5382706 0.046737099087662486 0.28542695270122914 chr14 107349540 5737163 0.05344375951680836 2.799943188340866 chr15 102531392 4879681 0.0475920681931247 0.28847484593130435 chr16 90354753 4772735 0.05282217970315297 0.33679011516633955 chr17 81195210 4265641 0.05253562371474869 0.3341690333411298 chr18 78077248 4438649 0.056849455042267884 0.47857667562287864 chr19 59128983 2998906 0.050718037886766966 0.4784410862030688 chr20 63025520 3560653 0.056495416459872126 0.6172235006965913 chr21 48129895 3067492 0.06373361088778606 0.36330607073359367 chr22 51304566 1886582 0.03677220464159077 0.36336152996752596 chrMT 16571 253098 15.273550178021845 13.973857671923593 chrX 155270560 5034967 0.03242705507083893 0.247422732433165 chrY 59373566 1454425 0.024496170568565817 0.326375461193609