BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819069.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 = 2,130,384 number of mapped reads = 1,967,683 (92.36%) number of supplementary alignments = 8,989 (0.42%) number of secondary alignments = 0 number of mapped bases = 114,012,137 bp number of sequenced bases = 113,984,678 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 108,060 duplication rate = 4.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4569 >>>>>>> ACTG content number of A's = 28,979,569 bp (25.42%) number of C's = 22,705,875 bp (19.92%) number of T's = 35,111,110 bp (30.8%) number of G's = 27,185,755 bp (23.85%) number of N's = 2,369 bp (0%) GC percentage = 43.77% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 540,583 number of insertions = 6,302 mapped reads with insertion percentage = 0.32% number of deletions = 16,649 mapped reads with deletion percentage = 0.84% homopolymer indels = 42.91% >>>>>>> Coverage mean coverageData = 0.0368X std coverageData = 0.3035X There is a 3.1% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 8628029 0.03461587764710123 0.5084393629165733 chr2 243199373 7928106 0.032599204110612574 0.35410007830241996 chr3 198022430 7824396 0.03951267540752833 0.2304410862869512 chr4 191154276 7469133 0.03907384734621369 0.2415243672828122 chr5 180915260 6273432 0.03467607983981009 0.2184573304342536 chr6 171115067 8948050 0.05229258975774471 0.2805384206237493 chr7 159138663 7244805 0.04552510913077107 0.3166093056845447 chr8 146364022 5847997 0.039955153733066996 0.29768307424647433 chr9 141213431 4759259 0.0337025944791328 0.3118749986382056 chr10 135534747 5687324 0.04196211027715276 0.2656538019389064 chr11 135006516 5837415 0.043238024155811856 0.3287252986771106 chr12 133851895 5057403 0.0377835741511168 0.2290662476541222 chr13 115169878 4157053 0.03609496747057421 0.21986518099951155 chr14 107349540 2157026 0.020093481537042452 0.18469567984625626 chr15 102531392 3431746 0.03347019808333432 0.21388854958294784 chr16 90354753 1913451 0.02117709291950585 0.18793012051981248 chr17 81195210 3063047 0.0377244790671765 0.24041809985500612 chr18 78077248 3514870 0.04501785206363831 0.5301257597405704 chr19 59128983 1546711 0.02615825474285597 0.34729839539339247 chr20 63025520 1596100 0.025324662136861385 0.19895459066003748 chr21 48129895 1791192 0.037215788648614335 0.24235878797858024 chr22 51304566 1043954 0.020348169400750803 0.16504488040808196 chrMT 16571 5486 0.33106028604188037 0.6064975854728344 chrX 155270560 7934951 0.05110402770493003 0.3015724831115528 chrY 59373566 351201 0.005915107069701692 0.1078853323688944