BamQC report ----------------------------------- >>>>>>> Input bam file = SRR630577.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 = 31,132,806 number of mapped reads = 30,746,217 (98.76%) number of supplementary alignments = 69,387 (0.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,438,984 number of mapped paired reads (second in pair) = 15,307,233 number of mapped paired reads (both in pair) = 30,551,926 number of mapped paired reads (singletons) = 194,291 number of mapped bases = 3,004,446,478 bp number of sequenced bases = 3,002,304,723 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,065,608 duplication rate = 10.97% >>>>>>> Insert size mean insert size = 33,118.403 std insert size = 1,813,719.8055 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 53.9542 >>>>>>> ACTG content number of A's = 883,974,579 bp (29.44%) number of C's = 597,254,487 bp (19.89%) number of T's = 891,006,810 bp (29.68%) number of G's = 629,613,885 bp (20.97%) number of N's = 454,962 bp (0.02%) GC percentage = 40.86% >>>>>>> Mismatches and indels general error rate = 0.0092 number of mismatches = 26,825,536 number of insertions = 549,027 mapped reads with insertion percentage = 1.75% number of deletions = 1,552,937 mapped reads with deletion percentage = 4.91% homopolymer indels = 54% >>>>>>> Coverage mean coverageData = 0.9705X std coverageData = 5.1239X There is a 15.25% of reference with a coverageData >= 1X There is a 10.78% of reference with a coverageData >= 2X There is a 8.2% of reference with a coverageData >= 3X There is a 6.6% of reference with a coverageData >= 4X There is a 5.48% of reference with a coverageData >= 5X There is a 4.65% of reference with a coverageData >= 6X There is a 4.01% of reference with a coverageData >= 7X There is a 3.5% of reference with a coverageData >= 8X There is a 3.08% of reference with a coverageData >= 9X There is a 2.73% of reference with a coverageData >= 10X There is a 2.44% of reference with a coverageData >= 11X There is a 2.19% of reference with a coverageData >= 12X There is a 1.98% of reference with a coverageData >= 13X There is a 1.79% of reference with a coverageData >= 14X There is a 1.63% of reference with a coverageData >= 15X There is a 1.48% of reference with a coverageData >= 16X There is a 1.36% of reference with a coverageData >= 17X There is a 1.25% of reference with a coverageData >= 18X There is a 1.14% of reference with a coverageData >= 19X There is a 1.05% of reference with a coverageData >= 20X There is a 0.97% of reference with a coverageData >= 21X There is a 0.9% of reference with a coverageData >= 22X There is a 0.83% of reference with a coverageData >= 23X There is a 0.77% of reference with a coverageData >= 24X There is a 0.72% of reference with a coverageData >= 25X There is a 0.67% of reference with a coverageData >= 26X There is a 0.62% of reference with a coverageData >= 27X There is a 0.58% of reference with a coverageData >= 28X There is a 0.54% of reference with a coverageData >= 29X There is a 0.5% of reference with a coverageData >= 30X There is a 0.47% of reference with a coverageData >= 31X There is a 0.44% of reference with a coverageData >= 32X There is a 0.41% of reference with a coverageData >= 33X There is a 0.39% of reference with a coverageData >= 34X There is a 0.36% of reference with a coverageData >= 35X There is a 0.34% of reference with a coverageData >= 36X There is a 0.32% of reference with a coverageData >= 37X There is a 0.3% of reference with a coverageData >= 38X There is a 0.28% of reference with a coverageData >= 39X There is a 0.27% of reference with a coverageData >= 40X There is a 0.25% of reference with a coverageData >= 41X There is a 0.24% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.21% of reference with a coverageData >= 44X There is a 0.2% of reference with a coverageData >= 45X There is a 0.19% of reference with a coverageData >= 46X There is a 0.18% of reference with a coverageData >= 47X There is a 0.17% of reference with a coverageData >= 48X There is a 0.16% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 255114147 1.0235246194231147 6.156041291515169 chr2 243199373 252039224 1.0363481652561661 6.165019635577215 chr3 198022430 204645878 1.0334479684952862 4.621272318962488 chr4 191154276 173830068 0.909370544240402 5.140966708695334 chr5 180915260 181461284 1.0030181201961625 4.48401461313531 chr6 171115067 179873274 1.0511831433289274 4.863410254079441 chr7 159138663 171691593 1.078880454085504 4.91006026121505 chr8 146364022 178160318 1.2172412015297038 5.267552188448881 chr9 141213431 157226194 1.1133940510233762 6.245664474326786 chr10 135534747 133702050 0.9864780283981347 5.179059552736198 chr11 135006516 132876657 0.9842240281202427 5.166302308160114 chr12 133851895 124494169 0.9300889539143244 4.209387818797863 chr13 115169878 91203818 0.7919068734274426 3.941679483577883 chr14 107349540 84677289 0.7887997377538832 4.058212015461596 chr15 102531392 92341310 0.9006150038419453 4.437271679955967 chr16 90354753 77802210 0.861074901062482 5.8742465086078175 chr17 81195210 64053831 0.7888868198013159 4.041114786597519 chr18 78077248 75923721 0.9724179955727947 6.060031168961219 chr19 59128983 41391073 0.7000132743700327 4.315845247795816 chr20 63025520 77318295 1.2267775815257058 5.316683361175046 chr21 48129895 36318327 0.7545897825042004 5.281977523638331 chr22 51304566 30717343 0.5987253259290801 3.543660465746057 chrMT 16571 1713 0.10337336310421821 0.4264461931266297 chrX 155270560 181683337 1.1701080810167748 5.1514199575955555 chrY 59373566 5899355 0.0993599575945969 3.2469401463228498