BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153315.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 51,642,644 number of mapped reads = 51,214,387 (99.17%) number of supplementary alignments = 409,054 (0.79%) number of secondary alignments = 0 number of mapped bases = 4,977,372,029 bp number of sequenced bases = 4,976,515,112 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,216,979 duplication rate = 34.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.4096 >>>>>>> ACTG content number of A's = 1,319,367,508 bp (26.51%) number of C's = 1,162,185,643 bp (23.35%) number of T's = 1,347,187,488 bp (27.07%) number of G's = 1,146,293,720 bp (23.03%) number of N's = 1,480,753 bp (0.03%) GC percentage = 46.39% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 14,737,805 number of insertions = 537,913 mapped reads with insertion percentage = 1.04% number of deletions = 407,820 mapped reads with deletion percentage = 0.79% homopolymer indels = 49.66% >>>>>>> Coverage mean coverageData = 1.6078X std coverageData = 15.1364X There is a 20.91% of reference with a coverageData >= 1X There is a 10.7% of reference with a coverageData >= 2X There is a 5.98% of reference with a coverageData >= 3X There is a 4.49% of reference with a coverageData >= 4X There is a 3.61% of reference with a coverageData >= 5X There is a 3.16% of reference with a coverageData >= 6X There is a 2.85% of reference with a coverageData >= 7X There is a 2.63% of reference with a coverageData >= 8X There is a 2.46% of reference with a coverageData >= 9X There is a 2.32% of reference with a coverageData >= 10X There is a 2.19% of reference with a coverageData >= 11X There is a 2.08% of reference with a coverageData >= 12X There is a 1.99% of reference with a coverageData >= 13X There is a 1.9% of reference with a coverageData >= 14X There is a 1.82% of reference with a coverageData >= 15X There is a 1.75% of reference with a coverageData >= 16X There is a 1.68% of reference with a coverageData >= 17X There is a 1.62% of reference with a coverageData >= 18X There is a 1.56% of reference with a coverageData >= 19X There is a 1.51% of reference with a coverageData >= 20X There is a 1.46% of reference with a coverageData >= 21X There is a 1.41% of reference with a coverageData >= 22X There is a 1.37% of reference with a coverageData >= 23X There is a 1.32% of reference with a coverageData >= 24X There is a 1.28% of reference with a coverageData >= 25X There is a 1.25% of reference with a coverageData >= 26X There is a 1.21% of reference with a coverageData >= 27X There is a 1.18% of reference with a coverageData >= 28X There is a 1.14% of reference with a coverageData >= 29X There is a 1.11% of reference with a coverageData >= 30X There is a 1.08% of reference with a coverageData >= 31X There is a 1.05% of reference with a coverageData >= 32X There is a 1.03% of reference with a coverageData >= 33X There is a 1% of reference with a coverageData >= 34X There is a 0.98% of reference with a coverageData >= 35X There is a 0.95% of reference with a coverageData >= 36X There is a 0.93% of reference with a coverageData >= 37X There is a 0.91% of reference with a coverageData >= 38X There is a 0.89% of reference with a coverageData >= 39X There is a 0.87% of reference with a coverageData >= 40X There is a 0.85% of reference with a coverageData >= 41X There is a 0.83% of reference with a coverageData >= 42X There is a 0.81% of reference with a coverageData >= 43X There is a 0.79% of reference with a coverageData >= 44X There is a 0.77% of reference with a coverageData >= 45X There is a 0.76% of reference with a coverageData >= 46X There is a 0.74% of reference with a coverageData >= 47X There is a 0.72% of reference with a coverageData >= 48X There is a 0.71% of reference with a coverageData >= 49X There is a 0.69% of reference with a coverageData >= 50X There is a 0.68% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 549179694 2.20332327276328 21.033126924063303 chr2 243199373 336328393 1.382932812906553 11.309623445917653 chr3 198022430 257779150 1.3017674310935383 10.510968588720859 chr4 191154276 193260075 1.011016227541779 9.660726645284898 chr5 180915260 298867530 1.6519752396785103 14.366822163213122 chr6 171115067 161963194 0.9465162644035314 8.997876707327475 chr7 159138663 233731418 1.4687280488211718 12.54203870322399 chr8 146364022 312330826 2.1339316980507683 25.173081319866352 chr9 141213431 119341331 0.8451131748225846 7.902636886777724 chr10 135534747 244185645 1.8016460753049548 14.289349139367248 chr11 135006516 225013550 1.666686591630881 12.919779118947712 chr12 133851895 244853876 1.8292895741222042 14.449534163070583 chr13 115169878 60990355 0.5295686342569539 6.043843790573019 chr14 107349540 138473563 1.2899315916956886 11.139666230906041 chr15 102531392 230882243 2.251820037710987 17.13673310231533 chr16 90354753 244568928 2.70676328449484 22.071237979893137 chr17 81195210 199892139 2.461871075892285 16.12962476786373 chr18 78077248 53900157 0.6903439655045219 6.619947049302321 chr19 59128983 280144834 4.73785984108673 31.031491647925446 chr20 63025520 123220730 1.955092635491147 17.3905490002033 chr21 48129895 50790201 1.0552734636134153 10.055586737556885 chr22 51304566 68367779 1.3325866356612392 11.343816879579286 chrMT 16571 9862 0.5951360811055458 1.5666002127820888 chrX 155270560 345596135 2.225767299351532 20.698980315778382 chrY 59373566 3700421 0.062324385232310285 2.5626197429024327