BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR975328.sorted.bam
outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 3,501,394
number of mapped reads = 3,457,100 (98.73%)
number of supplementary alignments = 18,705 (0.53%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 1,727,585
number of mapped paired reads (second in pair) = 1,729,515
number of mapped paired reads (both in pair) = 3,443,132
number of mapped paired reads (singletons) = 13,968
number of mapped bases = 314,490,769 bp
number of sequenced bases = 314,297,839 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 207,878
duplication rate = 3%
>>>>>>> Insert size
mean insert size = 81,091.5313
std insert size = 2,753,666.6058
median insert size = 168
>>>>>>> Mapping quality
mean mapping quality = 52.5828
>>>>>>> ACTG content
number of A's = 92,137,184 bp (29.32%)
number of C's = 59,973,430 bp (19.08%)
number of T's = 95,714,051 bp (30.45%)
number of G's = 66,465,834 bp (21.15%)
number of N's = 7,340 bp (0%)
GC percentage = 40.23%
>>>>>>> Mismatches and indels
general error rate = 0.0084
number of mismatches = 2,503,933
number of insertions = 59,043
mapped reads with insertion percentage = 1.66%
number of deletions = 104,041
mapped reads with deletion percentage = 2.94%
homopolymer indels = 44.27%
>>>>>>> Coverage
mean coverageData = 0.1016X
std coverageData = 1.4235X
There is a 7.07% of reference with a coverageData >= 1X
There is a 1.92% of reference with a coverageData >= 2X
There is a 0.39% of reference with a coverageData >= 3X
There is a 0.12% of reference with a coverageData >= 4X
There is a 0.04% of reference with a coverageData >= 5X
There is a 0.02% of reference with a coverageData >= 6X
There is a 0.02% of reference with a coverageData >= 7X
There is a 0.01% 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 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% 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 33497533 0.1343929770991423 1.5237685266216243
chr2 243199373 28810292 0.1184636771246939 1.7504785816112964
chr3 198022430 24145837 0.1219348585915242 0.5137002981890594
chr4 191154276 15454194 0.08084670834148644 1.069752803852904
chr5 180915260 14710204 0.08130991271825273 0.3673388343614879
chr6 171115067 19788607 0.11564502966883682 0.9674558801441154
chr7 159138663 16389176 0.10298676444202626 1.3841207067056898
chr8 146364022 19652439 0.13427096858543558 0.711152916556826
chr9 141213431 9297492 0.06583999789651736 1.5765465302781618
chr10 135534747 13284291 0.0980139137309195 4.417152961563199
chr11 135006516 10059572 0.07451175171426541 0.6171184211003864
chr12 133851895 15157529 0.11324104899672881 0.4301213360226498
chr13 115169878 7075134 0.06143215676585157 0.30585097322869725
chr14 107349540 12849297 0.11969587387146699 0.47744510499948056
chr15 102531392 5996323 0.05848280105277416 0.30290259867856323
chr16 90354753 8048688 0.08907874497758851 1.7870180878291981
chr17 81195210 8753179 0.10780413031753967 1.5451737316190475
chr18 78077248 11441139 0.14653614584366498 1.8787125258465958
chr19 59128983 5373852 0.09088355197991482 0.7817119971391717
chr20 63025520 8536952 0.13545230566919558 0.5255230952711742
chr21 48129895 5114459 0.1062636641945718 0.5237876215987466
chr22 51304566 3073300 0.05990305034448591 0.3482268831333858
chrMT 16571 86274 5.206324301490556 4.519948325684197
chrX 155270560 14332333 0.09230554072839049 0.544834289943376
chrY 59373566 3562673 0.060004362884317916 1.4115400400667903