BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617400.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 29,964,957 (93.64%) number of supplementary alignments = 488,661 (1.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,087,098 number of mapped paired reads (second in pair) = 14,877,859 number of mapped paired reads (both in pair) = 29,399,726 number of mapped paired reads (singletons) = 565,231 number of mapped bases = 2,949,691,454 bp number of sequenced bases = 2,949,034,393 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,405,173 duplication rate = 4.2% >>>>>>> Insert size mean insert size = 58,247.9854 std insert size = 2,307,932.365 median insert size = 210 >>>>>>> Mapping quality mean mapping quality = 53.8872 >>>>>>> ACTG content number of A's = 880,319,525 bp (29.85%) number of C's = 592,897,703 bp (20.1%) number of T's = 871,813,092 bp (29.56%) number of G's = 603,683,266 bp (20.47%) number of N's = 320,807 bp (0.01%) GC percentage = 40.58% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 26,151,525 number of insertions = 421,085 mapped reads with insertion percentage = 1.39% number of deletions = 292,005 mapped reads with deletion percentage = 0.95% homopolymer indels = 37.45% >>>>>>> Coverage mean coverageData = 0.9528X std coverageData = 2.9296X There is a 29.56% of reference with a coverageData >= 1X There is a 16.96% of reference with a coverageData >= 2X There is a 10.86% of reference with a coverageData >= 3X There is a 7.51% of reference with a coverageData >= 4X There is a 5.46% of reference with a coverageData >= 5X There is a 4.11% of reference with a coverageData >= 6X There is a 3.18% of reference with a coverageData >= 7X There is a 2.52% of reference with a coverageData >= 8X There is a 2.03% of reference with a coverageData >= 9X There is a 1.66% of reference with a coverageData >= 10X There is a 1.37% of reference with a coverageData >= 11X There is a 1.15% of reference with a coverageData >= 12X There is a 0.97% of reference with a coverageData >= 13X There is a 0.83% of reference with a coverageData >= 14X There is a 0.71% of reference with a coverageData >= 15X There is a 0.62% of reference with a coverageData >= 16X There is a 0.54% of reference with a coverageData >= 17X There is a 0.47% of reference with a coverageData >= 18X There is a 0.42% of reference with a coverageData >= 19X There is a 0.37% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.29% of reference with a coverageData >= 22X There is a 0.26% of reference with a coverageData >= 23X There is a 0.23% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.19% of reference with a coverageData >= 26X There is a 0.17% of reference with a coverageData >= 27X There is a 0.15% of reference with a coverageData >= 28X There is a 0.14% of reference with a coverageData >= 29X There is a 0.13% of reference with a coverageData >= 30X There is a 0.12% of reference with a coverageData >= 31X There is a 0.11% of reference with a coverageData >= 32X There is a 0.1% of reference with a coverageData >= 33X There is a 0.09% of reference with a coverageData >= 34X There is a 0.08% of reference with a coverageData >= 35X There is a 0.08% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.07% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.06% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.05% of reference with a coverageData >= 42X There is a 0.05% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.04% of reference with a coverageData >= 45X There is a 0.04% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.03% of reference with a coverageData >= 50X There is a 0.03% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 190028468 0.7623991757276304 2.74931516122162 chr2 243199373 293841969 1.2082348954082214 3.109299151995333 chr3 198022430 249066641 1.257769844557508 3.414760311563449 chr4 191154276 141392776 0.7396788549998222 2.2695652094137193 chr5 180915260 188434875 1.041564293691975 2.8609700281448283 chr6 171115067 135132873 0.7897193120930724 2.5964014240358746 chr7 159138663 220882946 1.3879904596157127 3.240853445842599 chr8 146364022 130630252 0.8925024757791912 3.251161291218825 chr9 141213431 117898966 0.8348990968146649 2.6017449436401168 chr10 135534747 94664852 0.698454485623528 2.4146482825335718 chr11 135006516 218830859 1.6208910909159377 3.8231894105993045 chr12 133851895 140455544 1.049335491290579 2.8062026133002282 chr13 115169878 127650726 1.1083690303119016 2.7643575461075836 chr14 107349540 85654594 0.7979036892007176 2.8964412987677814 chr15 102531392 67864403 0.6618890241927078 2.3787723253021453 chr16 90354753 74685584 0.8265816851936942 3.3397477563886944 chr17 81195210 91494981 1.1268519534588308 3.7264228463280236 chr18 78077248 42039722 0.5384375484135916 1.98423040472777 chr19 59128983 42380679 0.7167496691089715 2.3502831470957197 chr20 63025520 101003015 1.6025732909462707 4.76629045423295 chr21 48129895 40397040 0.8393336407652666 2.51825728955779 chr22 51304566 23773346 0.4633768074365935 2.0713160659476753 chrMT 16571 181491 10.952326353267757 4.74367230588003 chrX 155270560 128921222 0.830300489674282 2.5575129902635303 chrY 59373566 2383630 0.040146316965364685 0.6188185248570498