BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514725.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 69,055,952 number of mapped reads = 67,549,475 (97.82%) number of supplementary alignments = 2,491,324 (3.61%) number of secondary alignments = 0 number of mapped bases = 6,364,566,397 bp number of sequenced bases = 6,361,009,543 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,119,713 duplication rate = 45.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.6237 >>>>>>> ACTG content number of A's = 1,683,933,082 bp (26.47%) number of C's = 1,461,077,390 bp (22.97%) number of T's = 1,702,091,687 bp (26.76%) number of G's = 1,464,281,895 bp (23.02%) number of N's = 49,625,489 bp (0.78%) GC percentage = 45.99% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 56,302,247 number of insertions = 2,271,935 mapped reads with insertion percentage = 3.25% number of deletions = 1,785,534 mapped reads with deletion percentage = 2.54% homopolymer indels = 45.46% >>>>>>> Coverage mean coverageData = 2.0559X std coverageData = 45.4515X There is a 6.87% of reference with a coverageData >= 1X There is a 4.48% of reference with a coverageData >= 2X There is a 3.53% of reference with a coverageData >= 3X There is a 3.08% of reference with a coverageData >= 4X There is a 2.79% of reference with a coverageData >= 5X There is a 2.58% of reference with a coverageData >= 6X There is a 2.42% of reference with a coverageData >= 7X There is a 2.28% of reference with a coverageData >= 8X There is a 2.17% of reference with a coverageData >= 9X There is a 2.07% of reference with a coverageData >= 10X There is a 1.98% of reference with a coverageData >= 11X There is a 1.9% of reference with a coverageData >= 12X There is a 1.83% of reference with a coverageData >= 13X There is a 1.77% of reference with a coverageData >= 14X There is a 1.71% of reference with a coverageData >= 15X There is a 1.65% of reference with a coverageData >= 16X There is a 1.6% of reference with a coverageData >= 17X There is a 1.55% of reference with a coverageData >= 18X There is a 1.51% of reference with a coverageData >= 19X There is a 1.47% of reference with a coverageData >= 20X There is a 1.43% of reference with a coverageData >= 21X There is a 1.39% of reference with a coverageData >= 22X There is a 1.35% of reference with a coverageData >= 23X There is a 1.32% of reference with a coverageData >= 24X There is a 1.29% of reference with a coverageData >= 25X There is a 1.26% of reference with a coverageData >= 26X There is a 1.23% of reference with a coverageData >= 27X There is a 1.2% of reference with a coverageData >= 28X There is a 1.18% of reference with a coverageData >= 29X There is a 1.15% of reference with a coverageData >= 30X There is a 1.13% of reference with a coverageData >= 31X There is a 1.11% of reference with a coverageData >= 32X There is a 1.09% of reference with a coverageData >= 33X There is a 1.06% of reference with a coverageData >= 34X There is a 1.04% of reference with a coverageData >= 35X There is a 1.02% of reference with a coverageData >= 36X There is a 1.01% of reference with a coverageData >= 37X There is a 0.99% of reference with a coverageData >= 38X There is a 0.97% of reference with a coverageData >= 39X There is a 0.95% of reference with a coverageData >= 40X There is a 0.94% of reference with a coverageData >= 41X There is a 0.92% of reference with a coverageData >= 42X There is a 0.9% of reference with a coverageData >= 43X There is a 0.89% of reference with a coverageData >= 44X There is a 0.88% of reference with a coverageData >= 45X There is a 0.86% of reference with a coverageData >= 46X There is a 0.85% of reference with a coverageData >= 47X There is a 0.84% of reference with a coverageData >= 48X There is a 0.82% of reference with a coverageData >= 49X There is a 0.81% of reference with a coverageData >= 50X There is a 0.8% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 424610662 1.7035490635748507 53.208213103345614 chr2 243199373 404477485 1.663151841267288 37.55049017234433 chr3 198022430 530788923 2.6804484875778973 27.809206739558913 chr4 191154276 580669745 3.0377020967085246 59.71957288763419 chr5 180915260 226464588 1.2517716194863828 22.068587906207167 chr6 171115067 333034100 1.9462581866037547 82.080893857115 chr7 159138663 419179866 2.63405421471965 43.787535013226204 chr8 146364022 141013338 0.9634426279977466 21.25947995207632 chr9 141213431 299310223 2.119559172809844 92.18298429814308 chr10 135534747 551724774 4.070725671550484 58.398733803476546 chr11 135006516 373380734 2.7656497261213673 30.068957695816586 chr12 133851895 544928871 4.0711330310265685 37.58824062069575 chr13 115169878 26802080 0.23271779449136865 7.595613031050463 chr14 107349540 94049803 0.8761081137376089 15.107480833138633 chr15 102531392 266003897 2.594365411521966 28.98408662900133 chr16 90354753 189225897 2.094255041569313 33.675497772157534 chr17 81195210 281009663 3.460914295313726 27.051647209233504 chr18 78077248 181996191 2.3309759970023536 21.33654164642271 chr19 59128983 243558239 4.119100763157046 91.45524851507743 chr20 63025520 20628684 0.3273068433231491 8.696319379861244 chr21 48129895 103985297 2.1605136890491865 37.50958151695654 chr22 51304566 17818042 0.347299341738901 4.522567819306401 chrMT 16571 1031304 62.23547160702432 48.19235009322203 chrX 155270560 50676437 0.32637505139415995 11.096754450409739 chrY 59373566 58197554 0.9801930037350292 18.5380915735828