Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 1,084,947 A→G 51.1% K384E (AAA→GAA)  ycdB → conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb1,084,9470AG51.1% 0.2 / 67.9 47K384E (AAA→GAA) ycdBconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (12/11);  new base G (10/14);  total (22/25)
Fisher's exact test for biased strand distribution p-value = 5.64e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.93e-01

TGGATATGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTATTTTTTTGCGCTGCC  >  W3110S.gb/1084882‑1085017
                                                                 |                                                                      
tGGATATGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACaagaaa                                                                     >  1:2312258/1‑69 (MQ=255)
tGGATATGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAgg                                                                   >  1:1646075/1‑71 (MQ=255)
   atatGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTc                                                                <  1:2573672/71‑1 (MQ=255)
   atatGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTc                                                                <  1:229799/71‑1 (MQ=255)
   atatGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTc                                                                <  1:4172467/71‑1 (MQ=255)
    tatGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTc                                                                <  1:2637092/70‑1 (MQ=255)
    tatGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTc                                                                <  1:2631412/70‑1 (MQ=255)
           ttGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACaaaa                                                                       <  1:1682434/56‑1 (MQ=255)
           ttGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACaaaa                                                                       <  1:4983390/56‑1 (MQ=255)
           ttGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTc                                                                <  1:3935645/63‑1 (MQ=255)
            tGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCg                                                         >  1:3193155/1‑69 (MQ=255)
             gCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGGTTCCTGACAGTACAAAAAAGGCTc                                                                <  1:5141823/61‑1 (MQ=255)
             gCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAg                                                      >  1:4281119/1‑71 (MQ=255)
             gCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTc                                                                <  1:2078959/61‑1 (MQ=255)
                 tttGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAgcg                                                    <  1:3952342/69‑1 (MQ=255)
                 tttGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAg                                                                    <  1:4619023/53‑1 (MQ=255)
                 tttGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAg                                                                    <  1:3894400/53‑1 (MQ=255)
                  ttGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTg                                                 >  1:2376015/1‑71 (MQ=255)
                   tGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACaaaaaa                                                                     >  1:413407/1‑50 (MQ=255)
                   tGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACaaaaaa                                                                     >  1:536970/1‑50 (MQ=255)
                   tGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGaa                                                       >  1:3814607/1‑64 (MQ=255)
                   tGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCt                                                  >  1:5070133/1‑69 (MQ=255)
                   tGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTg                                                 >  1:4327661/1‑70 (MQ=255)
                   tGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCaa                                                              >  1:2237900/1‑57 (MQ=255)
                   tGTCTGCTA‑CAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGaa                                                       >  1:2380093/1‑63 (MQ=255)
                    gTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTgg                                                <  1:4315024/70‑1 (MQ=255)
                          tACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTc                                                                <  1:871412/48‑1 (MQ=255)
                          tACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTc                                                                <  1:1151061/48‑1 (MQ=255)
                            ccAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATa                                         <  1:4519740/69‑1 (MQ=255)
                              aaCACGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTgg                                                >  1:2928167/1‑60 (MQ=255)
                              aaCACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGt                                      >  1:2127940/1‑70 (MQ=255)
                               acacGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATgg                                                           <  1:2642614/48‑1 (MQ=255)
                               acacGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGACGCGCTGGAGGAATACGtt                                     >  1:4097586/1‑70 (MQ=255)
                               acacGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTa                                    <  1:197098/71‑1 (MQ=255)
                                cacGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTaa                                   <  1:2354104/71‑1 (MQ=255)
                                 acGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCg                                                         >  1:3245447/1‑48 (MQ=255)
                                 acGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTaaa                                  >  1:3448209/1‑71 (MQ=255)
                                  cGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATgg                                                           >  1:3482180/1‑45 (MQ=255)
                                  cGATCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAAc                                 <  1:3904196/71‑1 (MQ=255)
                                    aTCTGGAAAAAGGCTTCCTGACAGTACAAGAAAGGCTc                                                                <  1:3800341/38‑1 (MQ=255)
                                       tGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTaaa                                  >  1:2368997/1‑65 (MQ=255)
                                         gAAAAAGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATcgg                          >  1:1399858/1‑71 (MQ=255)
                                          aaaaaGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTa                              <  1:3482249/66‑1 (MQ=255)
                                          aaaaaGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATcggc                         <  1:595813/71‑1 (MQ=255)
                                          aaaaaGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATcggc                         <  1:1268420/71‑1 (MQ=255)
                                           aaaaGGCTTCCTGACAGTACAAGAAAGGCTCAATGGCGAAGCGCTgga                                               >  1:727893/1‑48 (MQ=255)
                                                        aCAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTAtttttt           >  1:3925534/1‑71 (MQ=255)
                                                            tACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTaaa                                  <  1:2948337/44‑1 (MQ=255)
                                                             aCAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTAt                             >  1:189825/1‑48 (MQ=255)
                                                              cAAGAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTAtttt             <  1:2308732/63‑1 (MQ=255)
                                                              cAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAAc                                 >  1:3750867/1‑43 (MQ=255)
                                                              cAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTATTTTTTTGCGCt     >  1:1757313/1‑71 (MQ=255)
                                                                aaaaaGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTATTTTTTTGCGCTGc   >  1:3050150/1‑71 (MQ=255)
                                                                aaaaaGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTATTTTTTTGCGCTGc   <  1:1438748/71‑1 (MQ=255)
                                                                 aaaaGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTATTTTTTTGCGCTGcc  <  1:1339084/71‑1 (MQ=255)
                                                                 |                                                                      
TGGATATGGGGTTGCTGTTTGTCTGCTACCAACACGATCTGGAAAAAGGCTTCCTGACAGTACAAAAAAGGCTCAATGGCGAAGCGCTGGAGGAATACGTTAAACCTATCGGCGGCGGTTATTTTTTTGCGCTGCC  >  W3110S.gb/1084882‑1085017

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A