BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927019.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 9,399,402 number of mapped reads = 9,177,419 (97.64%) number of supplementary alignments = 302,203 (3.22%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,593,280 number of mapped paired reads (second in pair) = 4,584,139 number of mapped paired reads (both in pair) = 9,040,090 number of mapped paired reads (singletons) = 137,329 number of mapped bases = 850,228,121 bp number of sequenced bases = 849,569,335 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 464,098 duplication rate = 3.89% >>>>>>> Insert size mean insert size = 361,005.7701 std insert size = 5,903,588.8067 median insert size = 187 >>>>>>> Mapping quality mean mapping quality = 52.3961 >>>>>>> ACTG content number of A's = 244,291,262 bp (28.75%) number of C's = 166,563,783 bp (19.61%) number of T's = 248,091,493 bp (29.2%) number of G's = 190,454,844 bp (22.42%) number of N's = 167,953 bp (0.02%) GC percentage = 42.02% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 8,174,184 number of insertions = 150,568 mapped reads with insertion percentage = 1.61% number of deletions = 446,791 mapped reads with deletion percentage = 4.74% homopolymer indels = 51.86% >>>>>>> Coverage mean coverageData = 0.2746X std coverageData = 1.4345X There is a 17.4% of reference with a coverageData >= 1X There is a 6.04% of reference with a coverageData >= 2X There is a 2.07% of reference with a coverageData >= 3X There is a 0.81% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.15% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 67669393 0.2714913717306245 1.7862869732312254 chr2 243199373 75262826 0.3094696547593484 2.2335467600895242 chr3 198022430 58398533 0.294908677769483 0.7651918918877877 chr4 191154276 53248490 0.27856290277283674 0.9653001525112266 chr5 180915260 52183163 0.288439808781194 0.7314503927761021 chr6 171115067 49866992 0.2914237353511366 0.809729202035389 chr7 159138663 44407400 0.27904846731054916 0.9633334277303727 chr8 146364022 42651144 0.2914045638893416 0.8292277032126694 chr9 141213431 36043769 0.25524320700061454 1.6565913579447342 chr10 135534747 42024903 0.3100673733503926 3.533917752221544 chr11 135006516 40618709 0.3008648041847106 1.4484322647608976 chr12 133851895 37775120 0.28221580277216096 0.7351045141775088 chr13 115169878 25646754 0.222686299971595 0.6402574743762456 chr14 107349540 25084696 0.2336730646447111 0.6754139281796173 chr15 102531392 24228822 0.23630637922091216 0.6729802647918462 chr16 90354753 26190542 0.2898634673928 2.0558512964438367 chr17 81195210 20418864 0.2514786771288602 0.8068187178776497 chr18 78077248 23085643 0.295676955724669 1.723201923427116 chr19 59128983 13608879 0.23015581039166527 1.1860093004728847 chr20 63025520 19743616 0.31326383344397635 0.8088575015866687 chr21 48129895 10813588 0.22467507980227258 0.8588620901788234 chr22 51304566 9688852 0.18884970199338594 0.6226138565452124 chrMT 16571 29350 1.7711664956852333 2.0461889415912062 chrX 155270560 49914755 0.32146953678791396 0.9007259005190392 chrY 59373566 1623318 0.027340752953932394 0.9476246991824612