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
A13 F1 I1 R1 778 68.7 3228504 93.4% 3015422 109.7

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% 166.4 / NA 52*335* (TAG→TAA) ldtEmurein L,D‑transpeptidase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (29/23);  total (29/23)

CGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGCTACTGCGTCACGCGTAACATATTCCCTTGCTCTGGTTCACCATTCTGCGCTGACTCTACTGAAGGCGCATTGCTGGCTGCGGGAGTTGCTCCACTGCTCACCGAAACCGGATACCCTGCCCGAC  >  NC_000913/1757603‑1757845
                                                                                                                      |                                                                                                                            
cGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATAGCGCAAGGAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACat                                                                                                          >  1:931494/1‑139 (MQ=255)
cGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACat                                                                                                          >  1:1089283/1‑139 (MQ=255)
       cGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCt                                                                                                   <  1:1610192/139‑1 (MQ=255)
              aCCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACata                                                                                                         <  2:44888/126‑1 (MQ=255)
              aCCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACata                                                                                                         >  1:44888/1‑126 (MQ=255)
               ccAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcac                                                                                           <  1:191107‑M1/139‑5 (MQ=255)
                        ggACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTg                                                                                                 <  2:452352/124‑1 (MQ=255)
                        ggACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTg                                                                                                 >  1:452352/1‑124 (MQ=255)
                        ggACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcg                                                                                  >  2:559637‑M1/1‑126 (MQ=255)
                         gACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgc                                                                                 <  1:559637‑M1/139‑15 (MQ=255)
                          acaacaTGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCTCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgct                                                                                <  1:594472‑M1/139‑16 (MQ=255)
                             acaTGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGGCGTTTACCGTTACTGCGTCAcgcg                                                                                                                >  1:974931/1‑104 (MQ=255)
                             acaTGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCAcgcg                                                                                                                <  2:974931/104‑1 (MQ=255)
                              caTGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgact                                                                            >  2:323148‑M1/1‑120 (MQ=255)
                                         aaTACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgc                                                                                   >  2:301341‑M1/1‑109 (MQ=255)
                                         aaTACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgc                                                                                   <  1:301341‑M1/121‑13 (MQ=255)
                                                cAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTc                                                                                                                     <  1:663591/80‑1 (MQ=255)
                                                cAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTc                                                                                                                     >  2:663591/1‑80 (MQ=255)
                                                cAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCAcg                                                                                                                  <  1:490840/83‑1 (MQ=255)
                                                cAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCAcg                                                                                                                  >  2:490840/1‑83 (MQ=255)
                                                cAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgc                                                          >  2:34512‑M1/1‑102 (MQ=255)
                                                           aCCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTg                                                                                                 <  2:74149/89‑1 (MQ=255)
                                                           aCCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTg                                                                                                 >  1:74149/1‑89 (MQ=255)
                                                            ccTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgct                                                                                <  2:96403‑M1/105‑16 (MQ=255)
                                                            ccTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgct                                                                                >  1:96403‑M1/1‑90 (MQ=255)
                                                             cTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcg                                                  <  1:1173831‑M1/134‑46 (MQ=255)
                                                             cTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcg                                                  >  2:1173831‑M1/1‑89 (MQ=255)
                                                               gtgaagtgaaAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttg                                           >  1:536488‑M1/1‑87 (MQ=255)
                                                               gtgaagtgaaAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcactgactctactgaaggcgcattgctggctgcgggagttg                                           >  2:1487680‑M1/1‑87 (MQ=255)
                                                                  aagtgaaAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCg                                                                                                                       <  2:606609/60‑1 (MQ=255)
                                                                  aagtgaaAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCg                                                                                                                       >  1:606609/1‑60 (MQ=255)
                                                                  aagtgaaAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctc                                        <  2:843515‑M1/139‑56 (MQ=255)
                                                                     tgaaAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTcc                                                                                                     >  2:348168/1‑75 (MQ=255)
                                                                     tgaaAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTcc                                                                                                     <  1:348168/75‑1 (MQ=255)
                                                                                 cacaTTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaa                         >  2:1549099‑M1/1‑69 (MQ=255)
                                                                                      tgtgCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTTCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccgga                    >  1:1350109‑M1/1‑64 (MQ=255)
                                                                                      tgtgCGCCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccgga                    >  2:96430‑M1/1‑64 (MQ=255)
                                                                                          cgcCATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggatacc                >  1:687299‑M1/1‑60 (MQ=255)
                                                                                             cATTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggataccctg             >  2:1191781‑M1/1‑57 (MQ=255)
                                                                                              aTTTTTTTTGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggataccctgc            >  2:42681‑M1/1‑56 (MQ=255)
                                                                                               ttttttttGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactga                                                                     >  2:553729‑M1/1‑55 (MQ=255)
                                                                                               ttttttttGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactga                                                                     <  1:553729‑M1/81‑27 (MQ=255)
                                                                                                  tttttGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggataccctgcccga        <  2:1350109‑M1/139‑88 (MQ=255)
                                                                                                  tttttGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggataccctgcccga        <  1:34512‑M1/139‑88 (MQ=255)
                                                                                                  tttttGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggataccctgcccga        >  1:783819‑M1/1‑52 (MQ=255)
                                                                                                  tttttGTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggataccctgcccga        >  2:412384‑M1/1‑52 (MQ=255)
                                                                                                       gTCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggataccctgcccgacgata   <  1:42681‑M1/139‑93 (MQ=255)
                                                                                                        tCTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcactgactctactgaaggcgcattgctggctgcgggagttgctccactgctcaccgaaaccggataccctgcccgacgatac  <  1:1487680‑M1/139‑94 (MQ=255)
                                                                                                         cTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgac                                                                             >  2:504673‑M1/1‑45 (MQ=255)
                                                                                                         cTGCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgac                                                                             <  1:504673‑M1/63‑19 (MQ=255)
                                                                                                           gCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgact                                                                            >  1:1191464‑M1/1‑43 (MQ=255)
                                                                                                           gCCGTTTACCGTTACTGCGTCACGCGTAACATATTCCCTTGCTtcaccattctgcgctgact                                                                            <  2:1191464‑M1/62‑20 (MQ=255)
                                                                                                                      |                                                                                                                            
CGCAGCTCGTGCTAACCAGCGTCTGGACAACATGGCTACTAAATACCGCAAGTAATAGTACCTGTGAAGTGAAAAATGGCGCACATTGTGCGCCATTTTTTTTGTCTGCCGTTTACCGCTACTGCGTCACGCGTAACATATTCCCTTGCTCTGGTTCACCATTCTGCGCTGACTCTACTGAAGGCGCATTGCTGGCTGCGGGAGTTGCTCCACTGCTCACCGAAACCGGATACCCTGCCCGAC  >  NC_000913/1757603‑1757845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A