BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173946.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 13,803,066 number of mapped reads = 13,447,796 (97.43%) number of supplementary alignments = 1,890,845 (13.7%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,731,710 number of mapped paired reads (second in pair) = 6,716,086 number of mapped paired reads (both in pair) = 13,217,412 number of mapped paired reads (singletons) = 230,384 number of mapped bases = 1,526,620,956 bp number of sequenced bases = 1,525,525,073 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,045,313 duplication rate = 65.89% >>>>>>> Insert size mean insert size = 1,162,584.9274 std insert size = 9,924,425.49 median insert size = 160 >>>>>>> Mapping quality mean mapping quality = 52.3604 >>>>>>> ACTG content number of A's = 453,999,740 bp (29.76%) number of C's = 304,185,008 bp (19.94%) number of T's = 449,964,849 bp (29.5%) number of G's = 317,364,153 bp (20.8%) number of N's = 11,323 bp (0%) GC percentage = 40.74% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 13,879,351 number of insertions = 177,907 mapped reads with insertion percentage = 1.27% number of deletions = 458,639 mapped reads with deletion percentage = 3.32% homopolymer indels = 40.71% >>>>>>> Coverage mean coverageData = 0.4931X std coverageData = 8.9152X There is a 9.8% of reference with a coverageData >= 1X There is a 7.59% of reference with a coverageData >= 2X There is a 5.85% of reference with a coverageData >= 3X There is a 4.74% of reference with a coverageData >= 4X There is a 3.63% of reference with a coverageData >= 5X There is a 2.98% of reference with a coverageData >= 6X There is a 2.28% of reference with a coverageData >= 7X There is a 1.94% of reference with a coverageData >= 8X There is a 1.49% of reference with a coverageData >= 9X There is a 1.32% of reference with a coverageData >= 10X There is a 1.01% of reference with a coverageData >= 11X There is a 0.92% of reference with a coverageData >= 12X There is a 0.7% of reference with a coverageData >= 13X There is a 0.64% of reference with a coverageData >= 14X There is a 0.49% of reference with a coverageData >= 15X There is a 0.45% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.31% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.17% of reference with a coverageData >= 21X There is a 0.16% of reference with a coverageData >= 22X There is a 0.12% of reference with a coverageData >= 23X There is a 0.11% of reference with a coverageData >= 24X There is a 0.09% of reference with a coverageData >= 25X There is a 0.08% of reference with a coverageData >= 26X There is a 0.07% of reference with a coverageData >= 27X There is a 0.06% of reference with a coverageData >= 28X There is a 0.05% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% 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 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 122270137 0.4905509824186155 4.152048892613854 chr2 243199373 138599208 0.5698995284827482 29.540123549194817 chr3 198022430 106081942 0.5357066974685646 2.267339857173399 chr4 191154276 102632134 0.5369073407492072 4.3383876659474065 chr5 180915260 90900461 0.5024477260790494 2.1857894234521207 chr6 171115067 90080820 0.5264341801064193 2.9696568957621334 chr7 159138663 82994111 0.5215207256077048 3.9766781695845332 chr8 146364022 79526454 0.5433470118770035 5.078532311078493 chr9 141213431 64202600 0.4546493881307933 3.701079548600737 chr10 135534747 78077272 0.5760683051999942 5.262088308198937 chr11 135006516 70225838 0.5201662858998598 2.4534978605841733 chr12 133851895 68178645 0.5093588327606419 2.397884014298028 chr13 115169878 49161694 0.42686243012257075 2.012573700180998 chr14 107349540 46382152 0.43206661155697546 2.0985505198737324 chr15 102531392 43983927 0.42898010201597575 2.1565021455668485 chr16 90354753 47540551 0.526154401639502 3.427748540107469 chr17 81195210 42232127 0.5201307687978145 2.6895916592044156 chr18 78077248 42201259 0.540506486601577 5.655100815835498 chr19 59128983 30500398 0.5158282191324007 3.185297233559242 chr20 63025520 33521277 0.5318683130262154 2.613634497303498 chr21 48129895 21832146 0.45360884331868995 3.3740352549235793 chr22 51304566 19728843 0.3845436096272601 2.3912767461799387 chrMT 16571 1964087 118.52555669543177 90.31532109698662 chrX 155270560 41283137 0.26587871519237133 1.645963327614216 chrY 59373566 12519736 0.2108638042727634 3.532647132664794