BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618626.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 30,205,806 number of mapped reads = 28,592,736 (94.66%) number of supplementary alignments = 177,798 (0.59%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,561,525 number of mapped paired reads (second in pair) = 14,031,211 number of mapped paired reads (both in pair) = 27,719,656 number of mapped paired reads (singletons) = 873,080 number of mapped bases = 2,658,857,380 bp number of sequenced bases = 2,656,970,376 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,613,806 duplication rate = 16.87% >>>>>>> Insert size mean insert size = 120,174.3368 std insert size = 3,432,012.3699 median insert size = 221 >>>>>>> Mapping quality mean mapping quality = 53.311 >>>>>>> ACTG content number of A's = 717,716,630 bp (27.01%) number of C's = 579,815,074 bp (21.82%) number of T's = 729,100,507 bp (27.44%) number of G's = 630,272,228 bp (23.72%) number of N's = 65,937 bp (0%) GC percentage = 45.54% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 34,346,491 number of insertions = 502,003 mapped reads with insertion percentage = 1.72% number of deletions = 1,362,517 mapped reads with deletion percentage = 4.64% homopolymer indels = 52.57% >>>>>>> Coverage mean coverageData = 0.8589X std coverageData = 3.6301X There is a 23.14% of reference with a coverageData >= 1X There is a 14.19% of reference with a coverageData >= 2X There is a 9.69% of reference with a coverageData >= 3X There is a 7.05% of reference with a coverageData >= 4X There is a 5.32% of reference with a coverageData >= 5X There is a 4.14% of reference with a coverageData >= 6X There is a 3.28% of reference with a coverageData >= 7X There is a 2.65% of reference with a coverageData >= 8X There is a 2.16% of reference with a coverageData >= 9X There is a 1.79% of reference with a coverageData >= 10X There is a 1.49% of reference with a coverageData >= 11X There is a 1.26% of reference with a coverageData >= 12X There is a 1.07% of reference with a coverageData >= 13X There is a 0.91% of reference with a coverageData >= 14X There is a 0.78% of reference with a coverageData >= 15X There is a 0.68% of reference with a coverageData >= 16X There is a 0.59% of reference with a coverageData >= 17X There is a 0.51% of reference with a coverageData >= 18X There is a 0.45% of reference with a coverageData >= 19X There is a 0.39% of reference with a coverageData >= 20X There is a 0.35% of reference with a coverageData >= 21X There is a 0.31% of reference with a coverageData >= 22X There is a 0.27% of reference with a coverageData >= 23X There is a 0.24% of reference with a coverageData >= 24X There is a 0.22% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.18% of reference with a coverageData >= 27X There is a 0.16% 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 0.07% of reference with a coverageData >= 36X There is a 0.07% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.06% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.05% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% 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 0.03% 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 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 232559221 0.9330336673464096 3.892965001275697 chr2 243199373 219800023 0.903785319380737 4.700690019717396 chr3 198022430 168097989 0.848883578491588 2.7385025323819967 chr4 191154276 133158547 0.6966025023682965 2.810397055983699 chr5 180915260 149468796 0.8261812519297709 2.672642732982627 chr6 171115067 140969137 0.8238265599370043 2.7757251115088972 chr7 159138663 132752036 0.8341909721837992 2.768567460421044 chr8 146364022 128481173 0.8778193660187884 2.916570736452139 chr9 141213431 114829331 0.8131615398538118 3.472267676087198 chr10 135534747 132913605 0.9806607378696771 3.3118151428629803 chr11 135006516 134841264 0.9987759701909499 3.5186576514592263 chr12 133851895 122221613 0.9131108155024626 3.2494127252461906 chr13 115169878 72380727 0.628469251308923 2.3994743620538554 chr14 107349540 84268891 0.7849953618804515 2.986635814962157 chr15 102531392 85112738 0.8301139420793194 3.203194220275948 chr16 90354753 94535728 1.0462728839511077 9.183513569283239 chr17 81195210 89447448 1.1016345422346958 3.6902068845406863 chr18 78077248 66648250 0.8536193540018214 3.1879994889089986 chr19 59128983 57593560 0.9740326499442752 3.7098873171778806 chr20 63025520 73091861 1.1597184918109362 3.6607828629534787 chr21 48129895 35246892 0.7323284623828912 4.327169185270897 chr22 51304566 48900622 0.9531436636653353 3.6489313063836772 chrMT 16571 17195 1.0376561462796452 3.445945024128517 chrX 155270560 137195789 0.8835917703909872 2.802151194829051 chrY 59373566 4324944 0.07284292137682954 3.1072229717146467