BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716883.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 539,605 number of mapped reads = 494,099 (91.57%) number of supplementary alignments = 2,306 (0.43%) number of secondary alignments = 0 number of mapped bases = 28,878,096 bp number of sequenced bases = 28,869,972 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,846 duplication rate = 1.31% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9036 >>>>>>> ACTG content number of A's = 7,298,160 bp (25.28%) number of C's = 5,643,468 bp (19.55%) number of T's = 9,012,105 bp (31.22%) number of G's = 6,915,450 bp (23.95%) number of N's = 789 bp (0%) GC percentage = 43.5% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 141,964 number of insertions = 1,539 mapped reads with insertion percentage = 0.31% number of deletions = 5,220 mapped reads with deletion percentage = 1.05% homopolymer indels = 44.41% >>>>>>> Coverage mean coverageData = 0.0093X std coverageData = 0.1187X There is a 0.89% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 3385809 0.013583954119817419 0.18430590760713855 chr2 243199373 2427083 0.009979807801560409 0.14063252363218287 chr3 198022430 2552555 0.012890231677290295 0.11777971870740193 chr4 191154276 1334098 0.006979169014246901 0.08812458757862522 chr5 180915260 1253118 0.006926546715849177 0.08670337678985318 chr6 171115067 1846251 0.010789529130126221 0.11359572853133278 chr7 159138663 1620490 0.010182880573779862 0.13730076231552704 chr8 146364022 2037578 0.013921303693061946 0.12977677930630924 chr9 141213431 1187954 0.008412471757024302 0.10858816007403678 chr10 135534747 1468966 0.010838298167185128 0.13463431877384188 chr11 135006516 945226 0.007001336142916243 0.09692366324769904 chr12 133851895 1242270 0.00928092949300419 0.1006204586457306 chr13 115169878 637252 0.005533148172649796 0.07731345276215039 chr14 107349540 624121 0.005813914060553962 0.08355395823728433 chr15 102531392 827741 0.008073049471521853 0.09337386474141189 chr16 90354753 584609 0.0064701521567991005 0.08940131445790088 chr17 81195210 631153 0.007773278743906199 0.09221545269779707 chr18 78077248 781034 0.010003349503302165 0.16023070825408262 chr19 59128983 582339 0.009848621952452657 0.14274138461207686 chr20 63025520 528637 0.008387665821717932 0.09451497972589876 chr21 48129895 259839 0.005398702822850538 0.07832031258133998 chr22 51304566 441904 0.008613346422226826 0.095629971722175 chrMT 16571 5362 0.3235773338965663 0.5951232186558485 chrX 155270560 1608360 0.010358434979560838 0.11211143794889411 chrY 59373566 64347 0.0010837651220073257 0.03859390991009355