BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818872.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,731,851 number of mapped reads = 1,709,268 (98.7%) number of supplementary alignments = 30,633 (1.77%) number of secondary alignments = 0 number of mapped bases = 158,048,072 bp number of sequenced bases = 157,947,276 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 426,534 duplication rate = 21.57% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.3721 >>>>>>> ACTG content number of A's = 44,869,991 bp (28.41%) number of C's = 34,440,682 bp (21.81%) number of T's = 44,548,499 bp (28.2%) number of G's = 34,085,821 bp (21.58%) number of N's = 2,283 bp (0%) GC percentage = 43.39% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 958,016 number of insertions = 22,228 mapped reads with insertion percentage = 1.26% number of deletions = 52,283 mapped reads with deletion percentage = 2.99% homopolymer indels = 39.72% >>>>>>> Coverage mean coverageData = 0.0511X std coverageData = 0.5733X There is a 3.4% of reference with a coverageData >= 1X There is a 1.01% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.13% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 15037830 0.06033216663480249 0.8476079953197815 chr2 243199373 12019001 0.04942036178687023 0.8891482450172878 chr3 198022430 9691217 0.048939996342838535 0.30653588169236196 chr4 191154276 7910897 0.04138488118361527 0.358539028227273 chr5 180915260 7021188 0.038809263519285216 0.29507358235063597 chr6 171115067 7838966 0.04581107986241796 0.3280175967694585 chr7 159138663 14039167 0.08821971188736202 1.0669373568999876 chr8 146364022 13838480 0.09454837200360619 0.5241758354273315 chr9 141213431 5785435 0.040969438664796694 0.46898546980292893 chr10 135534747 7277198 0.053692489646215966 0.754699926193858 chr11 135006516 6931074 0.0513388109356144 0.3818935068663803 chr12 133851895 6203576 0.04634656834705254 0.30052576489240584 chr13 115169878 4839509 0.04202061410536529 0.28286784369495327 chr14 107349540 4703978 0.04381926555064884 0.311951389825632 chr15 102531392 4416068 0.043070399356325915 0.2856680814886052 chr16 90354753 3937720 0.04358066254688339 0.6561787298611997 chr17 81195210 3965551 0.0488397160374362 0.3916324763126553 chr18 78077248 3026849 0.03876736280459065 0.5568115695080483 chr19 59128983 2794603 0.04726282878905595 0.7190643762223485 chr20 63025520 6522748 0.103493759353354 0.47619530580078084 chr21 48129895 1553477 0.03227675855100037 0.28964219707267524 chr22 51304566 1516987 0.029568264937666563 0.2736695848269443 chrMT 16571 265908 16.046587411743406 10.603496948478764 chrX 155270560 6339176 0.04082664479344958 0.33368000377798984 chrY 59373566 571469 0.009624973510939194 0.6717253874389796