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
A6 F17 I0 R2 159 90.8 4763082 92.7% 4415377 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,546,001 C→T 12.2% M182I (ATG→ATA)  rfaF ← ADP‑heptose:LPS heptosyltransferase II

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,546,0010CT12.2% 209.6 / 17.9 74M182I (ATG→ATA) rfaFADP‑heptose:LPS heptosyltransferase II
Reads supporting (aligned to +/- strand):  ref base C (35/30);  new base T (7/2);  total (42/32)
Fisher's exact test for biased strand distribution p-value = 2.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.67e-01

CAGCTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCACCTGC  >  minE/2545932‑2546067
                                                                     |                                                                  
cAGCTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAatca                                                                   <  1:3359410/71‑1 (MQ=255)
cAGCTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAatca                                                                   <  1:594248/71‑1 (MQ=255)
 aGCTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAatcat                                                                  >  1:1609315/1‑71 (MQ=255)
   cTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCg                                                                <  1:2330424/71‑1 (MQ=255)
     ccGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCgg                                                               >  1:533611/1‑70 (MQ=255)
        cATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGt                                                           >  1:3582739/1‑71 (MQ=255)
         aTAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGtt                                                          <  1:868464/71‑1 (MQ=255)
          tAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAatcat                                                                  >  1:4151609/1‑62 (MQ=255)
          tAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAatcat                                                                  >  1:4603892/1‑62 (MQ=255)
           aGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCt                                                        >  1:4712654/1‑71 (MQ=255)
            gTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTc                                                         >  1:405645/1‑69 (MQ=255)
            gTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCt                                                        <  1:1492670/70‑1 (MQ=255)
            gTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCt                                                        <  1:4429108/70‑1 (MQ=255)
               gTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACg                                                            >  1:230831/1‑63 (MQ=255)
               gTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCtgat                                                     >  1:162103/1‑70 (MQ=255)
                tAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCtgatga                                                   <  1:3602246/71‑1 (MQ=255)
                tAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCtgatga                                                   <  1:3319189/71‑1 (MQ=255)
                tAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCtgatga                                                   <  1:1769439/71‑1 (MQ=255)
                tAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCtgatga                                                   <  1:4106470/71‑1 (MQ=255)
                tAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCtgatga                                                   <  1:4430246/71‑1 (MQ=255)
                   tgtgGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAg                                                <  1:1592098/71‑1 (MQ=255)
                   tgtgGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAg                                                <  1:3212634/71‑1 (MQ=255)
                   tgtgGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAg                                                <  1:2533582/71‑1 (MQ=255)
                     tgGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCtg                                                       >  1:3563363/1‑62 (MQ=255)
                        ccAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCg                                                                <  1:641559/50‑1 (MQ=255)
                         cAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGaaaa                                          >  1:3390226/1‑71 (MQ=255)
                           gCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCg                                                                <  1:1297638/47‑1 (MQ=255)
                           gCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCt                                                        <  1:877915/55‑1 (MQ=255)
                           gCGTTTTGCCGGACCAAACTCCGCACCCCGGCAAAAACCAATCATCg                                                                <  1:4525573/47‑1 (MQ=255)
                            cGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAAtt                                        >  1:1605816/1‑70 (MQ=255)
                            cGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAAtt                                        >  1:3919048/1‑70 (MQ=255)
                             gTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGa                                      <  1:2161640/71‑1 (MQ=255)
                              ttttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCtgat                                                     <  1:1349342/55‑1 (MQ=255)
                              ttttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGAt                                     <  1:3017572/71‑1 (MQ=255)
                               tttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCtgat                                                     <  1:314869/54‑1 (MQ=255)
                                ttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGAtt                                    <  1:1701226/70‑1 (MQ=255)
                                ttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGAtt                                    <  1:1051582/70‑1 (MQ=255)
                                ttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTa                                   >  1:3261103/1‑71 (MQ=255)
                                ttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTa                                   >  1:4513071/1‑71 (MQ=255)
                                ttGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTa                                   >  1:1424445/1‑71 (MQ=255)
                                    cGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGaaa                                                 >  1:3067947/1‑53 (MQ=255)
                                    cGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGaaa                                                 >  1:3720002/1‑53 (MQ=255)
                                     ggACCAAACTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTACAgg                               >  1:4667334/1‑70 (MQ=255)
                                     ggACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAgg                               >  1:3539872/1‑70 (MQ=255)
                                     ggACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAgg                               >  1:1047925/1‑70 (MQ=255)
                                      gACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGta                             >  1:3468954/1‑71 (MQ=255)
                                       aCCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGAt                                     >  1:2802629/1‑62 (MQ=255)
                                        ccAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGaaa                                           >  1:2934664/1‑55 (MQ=255)
                                        ccAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGaaa                                           >  1:4343775/1‑55 (MQ=255)
                                        ccAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGaaa                                           >  1:4306301/1‑55 (MQ=255)
                                           aaCTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGaa                                            <  1:2418039/51‑1 (MQ=255)
                                           aaCTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGaa                                            <  1:1255756/51‑1 (MQ=255)
                                           aaCTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGaa                                            <  1:3030242/51‑1 (MQ=255)
                                           aaCTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGa                        >  1:2355657/1‑71 (MQ=255)
                                           aaCTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGa                        >  1:1293649/1‑71 (MQ=255)
                                           aaCTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGa                        >  1:4344409/1‑71 (MQ=255)
                                            aCTCCGCACCCGGGCAAAAACCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGAt                       >  1:735788/1‑71 (MQ=255)
                                              tCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGAttt                     >  1:1787920/1‑71 (MQ=255)
                                                       gggCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTAc                                  >  1:3726017/1‑49 (MQ=255)
                                                       gggCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTAc                                  >  1:3115075/1‑49 (MQ=255)
                                                       gggCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTAc                                  >  1:3426067/1‑49 (MQ=255)
                                                       gggCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTAc                                  >  1:1663846/1‑49 (MQ=255)
                                                       gggCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTAc                                  >  1:4077453/1‑49 (MQ=255)
                                                        ggCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCtt             <  1:2074303/69‑1 (MQ=255)
                                                        ggCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCtt             <  1:3915304/69‑1 (MQ=255)
                                                           aaaaaCCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTc        <  1:2235067/71‑1 (MQ=255)
                                                            aaaaCCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTc        <  1:151967/70‑1 (MQ=255)
                                                            aaaaCCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCa       <  1:1758869/71‑1 (MQ=255)
                                                            aaaaCCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCa       >  1:3824965/1‑71 (MQ=255)
                                                             aaaCCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCAc      >  1:1692164/1‑71 (MQ=255)
                                                             aaaCCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCAc      >  1:3268759/1‑71 (MQ=255)
                                                              aaCCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCAc      >  1:1690063/1‑70 (MQ=255)
                                                              aaCCAATTATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCAc      >  1:1082002/1‑70 (MQ=255)
                                                              aaCCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCa       >  1:2635578/1‑69 (MQ=255)
                                                              aaCCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCAcc     >  1:387121/1‑71 (MQ=255)
                                                              aaCCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCAcc     >  1:2115633/1‑71 (MQ=255)
                                                              aaCCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCAcc     >  1:827814/1‑71 (MQ=255)
                                                                 cAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCACCTGc  <  1:3385324/71‑1 (MQ=255)
                                                                 cAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCACCTGc  <  1:1754168/71‑1 (MQ=255)
                                                                     |                                                                  
CAGCTCCGCATAGTGGTAGTGTGGCCAGCGTTTTGCCGGACCAAACTCCGCACCCGGGCAAAAACCAATCATCGGACGTTCTGATGAAAGCGAAAATTGATTACAGGTATATGATTTTTCACCTTCGCTCACCTGC  >  minE/2545932‑2546067

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