BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124900.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 6,859,862 number of mapped reads = 6,772,848 (98.73%) number of supplementary alignments = 31,964 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,392,988 number of mapped paired reads (second in pair) = 3,379,860 number of mapped paired reads (both in pair) = 6,745,632 number of mapped paired reads (singletons) = 27,216 number of mapped bases = 586,987,301 bp number of sequenced bases = 586,664,193 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 560,426 duplication rate = 5.74% >>>>>>> Insert size mean insert size = 41,901.85 std insert size = 1,942,396.2439 median insert size = 196 >>>>>>> Mapping quality mean mapping quality = 52.759 >>>>>>> ACTG content number of A's = 165,299,733 bp (28.18%) number of C's = 109,172,247 bp (18.61%) number of T's = 175,296,729 bp (29.88%) number of G's = 136,887,181 bp (23.33%) number of N's = 8,303 bp (0%) GC percentage = 41.94% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 4,400,500 number of insertions = 78,424 mapped reads with insertion percentage = 1.13% number of deletions = 196,555 mapped reads with deletion percentage = 2.85% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.1896X std coverageData = 1.6914X There is a 12.77% of reference with a coverageData >= 1X There is a 3.71% of reference with a coverageData >= 2X There is a 1.1% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.16% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 49884276 0.20013701791338767 1.5939728277703227 chr2 243199373 54917315 0.22581191029633124 1.7955864582148213 chr3 198022430 42762997 0.21595026886600674 0.6302556316569295 chr4 191154276 30220517 0.1580949044529875 1.259886803423611 chr5 180915260 21840406 0.12072174563936729 0.4594432281688332 chr6 171115067 36316426 0.21223394664597245 1.6382367392195194 chr7 159138663 32895028 0.2067067008097209 2.1272099148879002 chr8 146364022 38443669 0.26265791602802496 0.9374250747276573 chr9 141213431 30803664 0.21813551148686416 2.0947360500832857 chr10 135534747 30093453 0.22203496642820308 4.788766472682452 chr11 135006516 29930562 0.22169716608345036 2.024952623405513 chr12 133851895 27963384 0.20891287344120157 0.6088631743617848 chr13 115169878 22713451 0.19721694070041473 0.5962614596445289 chr14 107349540 18729349 0.17447069638118617 0.6327762450054218 chr15 102531392 13518854 0.13185087743663912 0.4881410992356212 chr16 90354753 11853897 0.1311928438341257 1.3833380572002674 chr17 81195210 9180611 0.11306838174320874 1.5093891270224602 chr18 78077248 17472492 0.22378468052562508 2.5844663677637625 chr19 59128983 8863763 0.14990555477674966 0.9609230155658951 chr20 63025520 13763636 0.21838195067648788 0.693625872127387 chr21 48129895 9372742 0.19473846764053818 0.819062287805572 chr22 51304566 5285604 0.10302404663163899 0.4461558767537008 chrMT 16571 127945 7.721018647033975 5.168611946806698 chrX 155270560 28584098 0.18409219365216434 0.9876847872928902 chrY 59373566 1449162 0.024407528427718154 1.3333472258901662