BamQC report ----------------------------------- >>>>>>> Input bam file = SRR22354868.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP408873/SRP408873.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 = 23,355,700 number of mapped reads = 22,898,206 (98.04%) number of supplementary alignments = 1,012,096 (4.33%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,460,546 number of mapped paired reads (second in pair) = 11,437,660 number of mapped paired reads (both in pair) = 22,851,178 number of mapped paired reads (singletons) = 47,028 number of mapped bases = 2,846,010,222 bp number of sequenced bases = 2,844,782,030 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,328,340 duplication rate = 57.21% >>>>>>> Insert size mean insert size = 389,133.7591 std insert size = 7,165,583.9401 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 53.654 >>>>>>> ACTG content number of A's = 786,638,561 bp (27.65%) number of C's = 607,515,703 bp (21.36%) number of T's = 805,952,222 bp (28.33%) number of G's = 644,629,525 bp (22.66%) number of N's = 46,019 bp (0%) GC percentage = 44.02% >>>>>>> Mismatches and indels general error rate = 0.0061 number of mismatches = 16,171,736 number of insertions = 414,690 mapped reads with insertion percentage = 1.7% number of deletions = 442,599 mapped reads with deletion percentage = 1.85% homopolymer indels = 43.8% >>>>>>> Coverage mean coverageData = 0.9193X std coverageData = 49.5036X There is a 27.63% of reference with a coverageData >= 1X There is a 21.02% of reference with a coverageData >= 2X There is a 11.94% of reference with a coverageData >= 3X There is a 9.28% of reference with a coverageData >= 4X There is a 5.15% of reference with a coverageData >= 5X There is a 4.07% of reference with a coverageData >= 6X There is a 2.25% of reference with a coverageData >= 7X There is a 1.78% of reference with a coverageData >= 8X There is a 0.98% of reference with a coverageData >= 9X There is a 0.77% of reference with a coverageData >= 10X There is a 0.44% of reference with a coverageData >= 11X There is a 0.34% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 233960727 0.9386565460151852 26.798496774843752 chr2 243199373 274591803 1.129081048247604 169.06680902773834 chr3 198022430 186342867 0.9410189896164793 2.377477902597968 chr4 191154276 186271424 0.9744559624708579 10.56542859835623 chr5 180915260 166553514 0.9206161713500564 2.0130883572850844 chr6 171115067 161524044 0.9439498626967782 4.147564690190782 chr7 159138663 158005449 0.9928790780402623 38.61040861298206 chr8 146364022 140278388 0.9584212437124746 6.074794749868824 chr9 141213431 122148053 0.8649889187948419 14.468208899879981 chr10 135534747 156187698 1.1523812266385092 27.940763038824045 chr11 135006516 132295409 0.9799186951835718 5.8542619392079125 chr12 133851895 122470085 0.9149671358780539 2.024748828689812 chr13 115169878 85317186 0.7407942726135388 1.7561187671932859 chr14 107349540 85718032 0.7984946372383152 4.0178841353687105 chr15 102531392 80334416 0.7835104394174225 1.810037781718967 chr16 90354753 89975336 0.9958008075125832 5.34832278832198 chr17 81195210 80851495 0.9957668069335617 5.476856154294025 chr18 78077248 76143766 0.9752362941890574 12.06016922550269 chr19 59128983 59568547 1.007433985461918 14.565744334717644 chr20 63025520 60516333 0.9601877620367115 4.136290622910419 chr21 48129895 40248925 0.8362562394952243 5.96902043295786 chr22 51304566 36858595 0.7184271863833718 3.14702903046548 chrMT 16571 3411444 205.86832418079777 39.83470487723603 chrX 155270560 75951729 0.48915730709028166 2.3949822693525458 chrY 59373566 30484957 0.5134432552021552 13.090510355311206