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
A4 F1 I1 R1 765 39.6 1867486 94.4% 1762906 108.0

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% 56.9 / NA 19*335* (TAG→TAA) ldtEmurein L,D‑transpeptidase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (10/9);  total (10/9)

GATGACGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGCTACTGCGTCACGCGTAACATATTCCCTTGCTCTGGTTCACCATTCTGCGCTGACTCTACTGAAGGCGCATTGCTGGCTGCGGGAGTTGCTCCACTGCTCACCGAAACCGGATACCCTGCCCGACGATA  >  NC_000913/1757598‑1757849
                                                                                                                            |                                                                                                                                
gATGACGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGt                                                                                                                   <  2:64253/139‑1 (MQ=255)
                        cGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccatt                                                                                           >  1:45610‑M1/1‑131 (MQ=255)
                                                tACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcg                                                                    <  2:722817‑M1/138‑32 (MQ=255)
                                                tACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcg                                                                    >  1:722817‑M1/1‑107 (MQ=255)
                                                               tACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcggg                                                    <  2:45610‑M1/139‑48 (MQ=255)
                                                                aCCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcggga                                                   >  1:214340‑M1/1‑91 (MQ=255)
                                                                   tgtgAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTccc                                                                                                        <  1:590750/84‑1 (MQ=255)
                                                                   tgtgAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTccc                                                                                                        >  2:590750/1‑84 (MQ=255)
                                                                   tgtgAAGTGAAAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCAc                                                                                                                       >  1:255304/1‑68 (MQ=255)
                                                                   tgtgAAGTGAAAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCAc                                                                                                                       <  2:255304/68‑1 (MQ=255)
                                                                     tgaagtgaaAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgc                                              >  1:824136‑M1/1‑86 (MQ=255)
                                                                         gtgaaAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCAcgcg                                                                                                                    <  2:862145/65‑1 (MQ=255)
                                                                         gtgaaAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCAcgcg                                                                                                                    >  1:862145/1‑65 (MQ=255)
                                                                                      cacaTTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTg                                                                                                     <  1:82300/67‑1 (MQ=255)
                                                                                      cacaTTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTg                                                                                                     >  2:82300/1‑67 (MQ=255)
                                                                                                   a‑TTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggataccctgc                >  1:839790‑M1/1‑56 (MQ=255)
                                                                                                               cTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgct                                             <  2:303822‑M1/99‑55 (MQ=255)
                                                                                                               cTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgct                                             >  1:303822‑M1/1‑45 (MQ=255)
                                                                                                                  ccGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggataccctgcccgacgatacaacg  <  1:55819‑M1/139‑98 (MQ=255)
                                                                                                                            |                                                                                                                                
GATGACGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCA‑TTTTTTTTGTCTGCCGTTTACCGCTACTGCGTCACGCGTAACATATTCCCTTGCTCTGGTTCACCATTCTGCGCTGACTCTACTGAAGGCGCATTGCTGGCTGCGGGAGTTGCTCCACTGCTCACCGAAACCGGATACCCTGCCCGACGATA  >  NC_000913/1757598‑1757849

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A