BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818989.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 = 1,936,132 number of mapped reads = 1,875,407 (96.86%) number of supplementary alignments = 29,233 (1.51%) number of secondary alignments = 0 number of mapped bases = 173,504,596 bp number of sequenced bases = 173,400,306 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 881,088 duplication rate = 39.95% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.2293 >>>>>>> ACTG content number of A's = 49,014,361 bp (28.27%) number of C's = 37,241,515 bp (21.48%) number of T's = 51,075,969 bp (29.46%) number of G's = 36,060,032 bp (20.8%) number of N's = 8,429 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,102,993 number of insertions = 28,109 mapped reads with insertion percentage = 1.46% number of deletions = 56,661 mapped reads with deletion percentage = 2.96% homopolymer indels = 42.52% >>>>>>> Coverage mean coverageData = 0.056X std coverageData = 0.6572X There is a 2.49% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.72% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.24% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.08% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 17295938 0.06939175489556754 1.1468029403674316 chr2 243199373 14106022 0.0580018847334775 0.9150141302845713 chr3 198022430 9365190 0.047293581843228565 0.4020194353401968 chr4 191154276 9657451 0.05052176285086084 0.47213767959806796 chr5 180915260 9155457 0.0506063280676268 0.42979116420253927 chr6 171115067 7405371 0.043277141690859985 0.457558780355216 chr7 159138663 8479458 0.05328345632764302 0.6903796497855633 chr8 146364022 15341423 0.10481689960665333 0.6768889308476812 chr9 141213431 7288431 0.05161287384908876 0.6047022319571546 chr10 135534747 9142306 0.06745359549754426 0.7668613916119411 chr11 135006516 5974279 0.04425178263247679 0.4576177271234491 chr12 133851895 7962387 0.05948654667907391 0.4625818051621033 chr13 115169878 3861466 0.033528437010239776 0.3474596073852218 chr14 107349540 4137377 0.0385411712057639 0.37999863971879827 chr15 102531392 4609461 0.04495658266299554 0.3995075376078101 chr16 90354753 5445350 0.06026633706806769 0.7068544244296233 chr17 81195210 6062369 0.07466412119631195 0.5710906705770987 chr18 78077248 4092529 0.052416409451316724 0.70089008018606 chr19 59128983 3525503 0.05962394110515989 1.0482781946990747 chr20 63025520 5528595 0.087719942651802 0.605898549053144 chr21 48129895 2467681 0.05127127329074788 0.4653512711456293 chr22 51304566 1434409 0.02795870059596645 0.34364583434084633 chrMT 16571 25988 1.5682819383259912 2.672343248512176 chrX 155270560 10507983 0.06767530818462947 0.5566074365727367 chrY 59373566 632172 0.010647364519085817 0.5960171191789346