BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173957.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 = 3,943,464 number of mapped reads = 3,854,014 (97.73%) number of supplementary alignments = 476,054 (12.07%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,928,540 number of mapped paired reads (second in pair) = 1,925,474 number of mapped paired reads (both in pair) = 3,795,900 number of mapped paired reads (singletons) = 58,114 number of mapped bases = 440,136,963 bp number of sequenced bases = 439,856,091 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,057,018 duplication rate = 65.23% >>>>>>> Insert size mean insert size = 862,934.6424 std insert size = 8,662,880.875 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 52.6161 >>>>>>> ACTG content number of A's = 130,938,813 bp (29.77%) number of C's = 87,830,062 bp (19.97%) number of T's = 129,774,778 bp (29.5%) number of G's = 91,308,796 bp (20.76%) number of N's = 3,642 bp (0%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 3,757,405 number of insertions = 48,761 mapped reads with insertion percentage = 1.22% number of deletions = 117,097 mapped reads with deletion percentage = 2.97% homopolymer indels = 41.26% >>>>>>> Coverage mean coverageData = 0.1422X std coverageData = 2.7581X There is a 3.08% of reference with a coverageData >= 1X There is a 2.34% of reference with a coverageData >= 2X There is a 1.76% of reference with a coverageData >= 3X There is a 1.41% of reference with a coverageData >= 4X There is a 1.05% of reference with a coverageData >= 5X There is a 0.86% of reference with a coverageData >= 6X There is a 0.63% of reference with a coverageData >= 7X There is a 0.54% of reference with a coverageData >= 8X There is a 0.4% of reference with a coverageData >= 9X There is a 0.36% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.17% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.07% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% 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 0.01% 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 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 35035159 0.1405619727623467 1.3911802255261518 chr2 243199373 39535738 0.1625651312842817 8.750607821521847 chr3 198022430 30053419 0.15176775176428245 1.16147677793568 chr4 191154276 30223316 0.15810954707599637 1.5844996948766408 chr5 180915260 27373251 0.1513042680866169 1.1523085571944152 chr6 171115067 26148284 0.15281111393890287 1.253277403437085 chr7 159138663 23589938 0.14823511493244101 1.414244759612036 chr8 146364022 21258985 0.1452473409073167 1.5687754516104622 chr9 141213431 19013841 0.13464612300228015 1.3029007599139515 chr10 135534747 22220156 0.16394435000494745 1.7594514938764778 chr11 135006516 20115446 0.14899611215802355 1.1616306582098603 chr12 133851895 20404465 0.15244061356023386 1.1729267317144938 chr13 115169878 14918392 0.12953380049599428 1.0758407535411456 chr14 107349540 13560949 0.12632517102541846 1.0565465956461524 chr15 102531392 12631147 0.12319297293847332 1.0522556235711713 chr16 90354753 13521731 0.1496515739465305 1.292114513150365 chr17 81195210 12404412 0.15277270666582426 1.1920958424790835 chr18 78077248 12087452 0.15481401188730423 1.7128702848457993 chr19 59128983 8433743 0.1426329791601523 1.2637375627485317 chr20 63025520 9556650 0.15163143437769336 1.1816043722683982 chr21 48129895 6258943 0.13004273123803822 1.2656190902581004 chr22 51304566 5927699 0.1155394044264988 1.1386987895079437 chrMT 16571 1084802 65.4638826866212 60.28428759702076 chrX 155270560 11447774 0.07372791081580436 0.7987119119406657 chrY 59373566 3331271 0.056106971914066946 1.049627144112605