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
A2 F1 I2 R1 764 42.0 2018750 95.5% 1927906 109.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,757,721 C→T *335* (TAG→TAA)  ldtE ← murein L,D‑transpeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,757,7210CT100.0% 59.2 / NA 20*335* (TAG→TAA) ldtEmurein L,D‑transpeptidase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (11/9);  total (11/9)

CTAAAGATGACGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGCTACTGCGTCACGCGTAACATATTCCCTTGCTCTGGTTCACCATTCTGCGCTGACTCTACTGAAGGCGCATTGCTGGCTGCGGGAGTTGCTCCACTGCTCACCGAAACCGGATACCCTGCCCGACGATACAAC  >  NC_000913/1757593‑1757853
                                                                                                                                |                                                                                                                                    
ctAAAGATGACGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGAACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCa                                                                                                                            >  2:627933/1‑139 (MQ=255)
 tAAAGATGACGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCAc                                                                                                                           >  1:147984/1‑139 (MQ=255)
   aaGATGACGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTATTAAATACCGGAAGTAATGGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCGATTTGTTTTGTCTGCCGTTTACCGTTACTGCGTCAcgc                                                                                                                         <  2:719620/139‑1 (MQ=255)
          cGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACTGTTACTGCGTCACGCGTAACat                                                                                                                  >  2:270559/1‑139 (MQ=255)
               cTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCAcgc                                                                                                                         >  1:214863/1‑127 (MQ=255)
               cTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCAcgc                                                                                                                         <  2:214863/127‑1 (MQ=255)
               cTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTcc                                                                                                             <  2:845740/139‑1 (MQ=255)
                   tGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTg                                                                                                         <  1:627933/139‑1 (MQ=255)
                                  ggACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcg                                                                                          <  2:147984‑M1/139‑14 (MQ=255)
                                           ggCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCg                                                                                                                               >  2:810417/1‑93 (MQ=255)
                                           ggCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCg                                                                                                                               <  1:810417/93‑1 (MQ=255)
                                                     tACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgct                                                                                        <  2:123813‑M1/122‑16 (MQ=255)
                                                     tACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgct                                                                                        >  1:123813‑M1/1‑107 (MQ=255)
                                                          cAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgc                                                                  >  1:82066‑M1/1‑102 (MQ=255)
                                                                       cTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagt                                                     >  1:873280‑M1/1‑89 (MQ=255)
                                                                         gtgaagtgaaAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttg                                                   >  2:775923‑M1/1‑87 (MQ=255)
                                                                                                          tttttttGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggataccctgccc                  >  2:141207‑M1/1‑54 (MQ=255)
                                                                                                                      ccGTTTACCGTTACTGCGTCACGCGTAACATATTCCCt                                                                                                           <  2:969099/38‑1 (MQ=255)
                                                                                                                      ccGTTTACCGTTACTGCGTCACGCGTAACATATTCCCt                                                                                                           >  1:969099/1‑38 (MQ=255)
                                                                                                                          ttACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggataccctgcccgacgatacaacgcttt  <  1:141207‑M1/139‑102 (MQ=255)
                                                                                                                                |                                                                                                                                    
CTAAAGATGACGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGCTACTGCGTCACGCGTAACATATTCCCTTGCTCTGGTTCACCATTCTGCGCTGACTCTACTGAAGGCGCATTGCTGGCTGCGGGAGTTGCTCCACTGCTCACCGAAACCGGATACCCTGCCCGACGATACAAC  >  NC_000913/1757593‑1757853

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A