BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081742.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,259,137 number of mapped reads = 2,027,086 (89.73%) number of supplementary alignments = 14,643 (0.65%) number of secondary alignments = 0 number of mapped bases = 135,930,725 bp number of sequenced bases = 135,883,942 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 76,857 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1834 >>>>>>> ACTG content number of A's = 37,569,730 bp (27.65%) number of C's = 25,561,609 bp (18.81%) number of T's = 42,617,357 bp (31.36%) number of G's = 30,133,649 bp (22.18%) number of N's = 1,597 bp (0%) GC percentage = 40.99% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 1,058,676 number of insertions = 9,299 mapped reads with insertion percentage = 0.45% number of deletions = 26,710 mapped reads with deletion percentage = 1.3% homopolymer indels = 47.77% >>>>>>> Coverage mean coverageData = 0.0439X std coverageData = 0.3236X There is a 3.76% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 10738920 0.043084827459667595 0.4819905767774247 chr2 243199373 11511597 0.04733399127636731 0.3922996184793428 chr3 198022430 9209543 0.04650757492471939 0.24405206288853765 chr4 191154276 9122866 0.04772514740920575 0.2576613630157288 chr5 180915260 8472779 0.04683285975986769 0.2447275477319188 chr6 171115067 8017824 0.04685632972343692 0.27592003482076694 chr7 159138663 7411553 0.046572924896321394 0.3899990483136347 chr8 146364022 6913254 0.047233287972914546 0.4495506863262211 chr9 141213431 5814144 0.041172740856356645 0.30645987951353626 chr10 135534747 6346602 0.04682638320046446 0.34039685907332895 chr11 135006516 6093477 0.04513468816571787 0.28978826481076464 chr12 133851895 6126023 0.045767174233879916 0.24312585801880948 chr13 115169878 4469509 0.038807968521074585 0.2233129487882542 chr14 107349540 4260386 0.03968704476982388 0.2343404902587928 chr15 102531392 3909962 0.03813429159334929 0.22660044289252146 chr16 90354753 3810817 0.04217616532026821 0.25438865136952044 chr17 81195210 3462638 0.04264584080760429 0.24749651818274576 chr18 78077248 3696610 0.04734554681025643 0.5204052484598912 chr19 59128983 2468202 0.041742676345371946 0.39165718625047014 chr20 63025520 2655423 0.042132504420431593 0.23601935129392468 chr21 48129895 1740862 0.036170076830626785 0.23008512404265272 chr22 51304566 1419251 0.02766324931001268 0.18684370313598075 chrMT 16571 7747 0.46750346991732544 0.6998043045913248 chrX 155270560 7920378 0.05101017217945243 0.27353770640083647 chrY 59373566 330358 0.005564058591326652 0.12315583863733988