BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818766.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 = 833,308 number of mapped reads = 486,275 (58.35%) number of supplementary alignments = 3,621 (0.43%) number of secondary alignments = 0 number of mapped bases = 32,992,127 bp number of sequenced bases = 32,975,760 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,525 duplication rate = 10.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1427 >>>>>>> ACTG content number of A's = 9,084,507 bp (27.55%) number of C's = 6,750,985 bp (20.47%) number of T's = 9,616,798 bp (29.16%) number of G's = 7,521,454 bp (22.81%) number of N's = 2,016 bp (0.01%) GC percentage = 43.28% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 170,683 number of insertions = 4,013 mapped reads with insertion percentage = 0.8% number of deletions = 9,275 mapped reads with deletion percentage = 1.88% homopolymer indels = 41.31% >>>>>>> Coverage mean coverageData = 0.0107X std coverageData = 0.1806X There is a 0.89% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% 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 2883681 0.011569403472017828 0.23139376108042645 chr2 243199373 2919512 0.012004603317788982 0.34247273775142306 chr3 198022430 1998493 0.010092255710628337 0.11514063936471226 chr4 191154276 2130185 0.011143799890722821 0.1630155586882534 chr5 180915260 2050844 0.01133593705694036 0.12827066398897843 chr6 171115067 1988352 0.011619970320906925 0.13913093994316114 chr7 159138663 1613567 0.010139377631946047 0.14295800944638654 chr8 146364022 1554930 0.010623717350429192 0.12922440361734294 chr9 141213431 1460290 0.01034101352583098 0.13178662928423662 chr10 135534747 1488565 0.010982903151765207 0.20339866537133267 chr11 135006516 1578864 0.01169472442352338 0.13402127226828384 chr12 133851895 1624950 0.01213991030907706 0.13780670237458942 chr13 115169878 945395 0.008208700195028425 0.10352854494647176 chr14 107349540 1029239 0.009587735541298081 0.1297283921264495 chr15 102531392 930080 0.009071173051078834 0.10940345021933995 chr16 90354753 1060149 0.011733184639440052 0.22094170003751187 chr17 81195210 1013521 0.012482522060106747 0.13482864691875202 chr18 78077248 821739 0.010524692161281095 0.15360941366629066 chr19 59128983 772553 0.013065555347028378 0.21272928383011877 chr20 63025520 819835 0.013007984702069892 0.14151503426537562 chr21 48129895 457760 0.009510928706576235 0.12482485925998688 chr22 51304566 445881 0.008690863889190681 0.11634011703425119 chrMT 16571 35099 2.1180978818417717 2.2383853896578088 chrX 155270560 977152 0.00629322132927195 0.1058762730877368 chrY 59373566 391491 0.006593691879648933 0.34710093952652216