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 703,790 G→T intergenic (‑179/‑154) nagB ← / → nagE glucosamine‑6‑phosphate deaminase/N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913703,7900GT100.0% 133.8 / NA 42intergenic (‑179/‑154)nagB/nagEglucosamine‑6‑phosphate deaminase/N‑acetyl glucosamine specific PTS enzyme IIC, IIB, and IIA components
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (20/22);  total (20/22)

CATCTTTAAGCGTAACCTGGATTTGCGCAGACAGGCGTCAATCCGACCTGATTTTTTGAATGATAAAATAAGTTTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAAGACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCGGCAGTACAATTTGCAGCAAAATAAAAATACGGCTTGAAACGAG  >  NC_000913/703655‑703914
                                                                                                                                       |                                                                                                                            
cATCTTTAAGCGTAACCTGGATTTGCGCAGACAGGCGTCAATCCGACCTGATTTTTTGAATGATAAAATAAGTTTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATaca                                                                                                                           <  2:153299/139‑1 (MQ=255)
             aaCCTGGATTTGCGCAGACAGGCGTCAATCCGACCTGATTTTTTGAATGATAAAATAAGTTTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTg                                                                                                              >  1:819183/1‑139 (MQ=255)
              aCCTGGATTTGCGCAGACAGGCGTCAATCCGACCTGATTTTTTGAATGATAAAATAAGTTTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGc                                                                                                             >  1:931763/1‑139 (MQ=255)
              aCCTGGATTTGCGCAGACAGGCGTCAATCCGACCTGATTTTTTGAATGATAAAATAAGTTTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGc                                                                                                             >  1:610424/1‑139 (MQ=255)
                cTGGATTTGCGCAGACAGGCGTCAATCCGACCTGATTTTTTGAATGATAAAATAAGTTTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGa                                                                                                           <  1:870797/139‑1 (MQ=255)
                 tGGATTTGCGCAGACAGGCGTCAATCCGACCTGATTTTTTGAATGATAAAATAAGTTTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGAt                                                                                                          <  2:931763/139‑1 (MQ=255)
                                     tCAATCCGACCTGATTTTTTGAATGATAAAATAAGTTTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTcacaca                                                                                      <  1:71317/139‑1 (MQ=255)
                                     tCAATCCGACCTGATTTTTTGAATGATAAAATAAGATTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTcacaca                                                                                      <  2:610424/139‑1 (MQ=255)
                                        aTCCGACCTGATTTTTTGAATGATAAAATAAGTTTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACActc                                                                                   >  2:1003028/1‑139 (MQ=255)
                                                 gATTTTTTGAATGATAAAATAAGTTTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAga                                                                          <  1:492437/139‑1 (MQ=255)
                                                             gATAAAATAAGTTTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAAt                                                              <  2:819183/139‑1 (MQ=255)
                                                                                  tAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAg                                                    >  1:401119/1‑128 (MQ=255)
                                                                                  tAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAg                                                    <  2:401119/128‑1 (MQ=255)
                                                                                    gCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCGGCAGTa                                       <  1:1003028/139‑1 (MQ=255)
                                                                                         tAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTcaca                                                                                        >  2:282985/1‑85 (MQ=255)
                                                                                         tAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTcaca                                                                                        <  1:282985/85‑1 (MQ=255)
                                                                                         tAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCg                                             <  1:179046/128‑1 (MQ=255)
                                                                                         tAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCg                                             >  2:179046/1‑128 (MQ=255)
                                                                                                   tGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGtt                                                                                                                     >  1:874721/1‑46 (MQ=255)
                                                                                                   tGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGtt                                                                                                                     <  2:874721/46‑1 (MQ=255)
                                                                                                   tGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTcaca                                                                                        <  2:868008/75‑1 (MQ=255)
                                                                                                   tGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTcaca                                                                                        >  1:868008/1‑75 (MQ=255)
                                                                                                   tGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTcaca                                                                                        >  1:465725/1‑75 (MQ=255)
                                                                                                   tGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTcaca                                                                                        <  2:465725/75‑1 (MQ=255)
                                                                                                   tGATAATAACGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCGGCAGTACAATTTGCAGCaaaa                        >  2:707664/1‑139 (MQ=255)
                                                                                                            cGATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCGGCAGTACAATTTGCAGCAAAATAAAAATAc               >  1:128758/1‑139 (MQ=255)
                                                                                                             gATATTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCGGCAGTACAATTTGCAGCAAAATAAAAATACg              >  2:204571/1‑139 (MQ=255)
                                                                                                               tatTTGGTGACAAAACTTACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTAc                                                      <  1:611590/97‑1 (MQ=255)
                                                                                                               tatTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTAc                                                      <  1:245471/97‑1 (MQ=255)
                                                                                                               tatTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTAc                                                      >  2:611590/1‑97 (MQ=255)
                                                                                                               tatTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTAc                                                      >  2:245471/1‑97 (MQ=255)
                                                                                                               tatTTGGTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCGGCAGTACAATTTg                                <  2:586393/119‑1 (MQ=255)
                                                                                                               taataggTGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCGGCAGTACAATTTg                                >  1:586393/6‑119 (MQ=255)
                                                                                                                      tGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGt                                                                                >  2:542587/1‑64 (MQ=255)
                                                                                                                      tGACAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGt                                                                                <  1:542587/64‑1 (MQ=255)
                                                                                                                         cAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTcaca                                                                                        <  1:1004559/53‑1 (MQ=255)
                                                                                                                         cAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTcaca                                                                                        >  2:1004559/1‑53 (MQ=255)
                                                                                                                         cAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCGGCAGTACAATTTGCAGCAAAATAAAAATACGGCTTGAAACGa   >  2:506044/1‑138 (MQ=255)
                                                                                                                         cAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCGGCAGTACAATTTGCAGCAAAATAAAAATACGGCTTGAAACGa   <  1:506044/138‑1 (MQ=255)
                                                                                                                         cAAAACTCACAAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCGGCAGTACAATTTGCAGCAAAATAAAAATACGGCTTGAAACGAg  <  1:204571/139‑1 (MQ=255)
                                                                                                                                  caAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACAct                                                                                    >  2:523879/1‑48 (MQ=255)
                                                                                                                                  caAAATACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACAct                                                                                    <  1:523879/48‑1 (MQ=255)
                                                                                                                                       |                                                                                                                            
CATCTTTAAGCGTAACCTGGATTTGCGCAGACAGGCGTCAATCCGACCTGATTTTTTGAATGATAAAATAAGTTTTCTGGTTTAGCCAGTAAAAGGGAGTGATAATAACGATATTTGGTGACAAAACTCACAAAAGACACGCGTTTAATTTGCGATACGAATTAAATTTTCACACACTCTGTAGCAGATGATCTAACAATCTGATTACAGAACATCGGCAGTACAATTTGCAGCAAAATAAAAATACGGCTTGAAACGAG  >  NC_000913/703655‑703914

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