BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716861.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 = 3,994,854 number of mapped reads = 3,733,118 (93.45%) number of supplementary alignments = 79,620 (1.99%) number of secondary alignments = 0 number of mapped bases = 286,409,039 bp number of sequenced bases = 286,302,710 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 295,813 duplication rate = 6.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0186 >>>>>>> ACTG content number of A's = 70,862,431 bp (24.75%) number of C's = 58,856,388 bp (20.56%) number of T's = 85,441,986 bp (29.84%) number of G's = 71,131,137 bp (24.84%) number of N's = 10,768 bp (0%) GC percentage = 45.4% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,851,555 number of insertions = 23,451 mapped reads with insertion percentage = 0.62% number of deletions = 51,086 mapped reads with deletion percentage = 1.35% homopolymer indels = 39.3% >>>>>>> Coverage mean coverageData = 0.0925X std coverageData = 0.7046X There is a 6.6% of reference with a coverageData >= 1X There is a 1.59% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% 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 30377028 0.12187342955506618 1.2749334705228792 chr2 243199373 26351204 0.1083522694772737 0.7183463044670385 chr3 198022430 18071792 0.0912613384251471 0.40785514795655337 chr4 191154276 15074443 0.07886008785908613 0.6147506837246247 chr5 180915260 16662769 0.09210261754591625 0.4220575433592616 chr6 171115067 16685198 0.09750864311673968 0.4570823701230869 chr7 159138663 26273839 0.16510028741412763 1.3839177842157713 chr8 146364022 17438683 0.11914596744273671 0.6972883571302434 chr9 141213431 7886664 0.05584924850384805 0.4465666145141435 chr10 135534747 14616310 0.10784179203876036 0.9743415765391541 chr11 135006516 8260461 0.06118564677278243 0.5288310971468773 chr12 133851895 9767938 0.07297571692952125 0.3595921956846348 chr13 115169878 5156284 0.04477111628094284 0.27437440856499 chr14 107349540 5461361 0.05087456359850261 0.3298261500306684 chr15 102531392 5909064 0.05763175438016096 0.31738451295704473 chr16 90354753 8669486 0.09594941839971606 0.4590836917122746 chr17 81195210 5218031 0.06426525653422166 0.40144731785533344 chr18 78077248 8151449 0.1044023605954964 0.6976652256110204 chr19 59128983 6929193 0.11718775883562889 0.9208853143126997 chr20 63025520 6304355 0.10002860745932758 0.4649166849071536 chr21 48129895 4045070 0.08404485403510646 0.5044431615966115 chr22 51304566 4227530 0.0824006580622863 0.40869080871031893 chrMT 16571 41608 2.5108925230824934 2.5082427323907286 chrX 155270560 17850217 0.11496201855651193 0.4937759771509949 chrY 59373566 979062 0.016489863519398514 0.5671073612297624