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
A9 F1 I2 R1 760 52.7 2744488 90.2% 2475528 105.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,850,810 (C)5→4 intergenic (+117/‑50) sppA → / → ansA protease IV (signal peptide peptidase)/cytoplasmic L‑asparaginase 1

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,850,8060C.100.0% 116.6 / NA 29intergenic (+113/‑54)sppA/ansAprotease IV (signal peptide peptidase)/cytoplasmic L‑asparaginase 1
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (14/15);  total (14/15)

CTGACCTGCGCCAACATGCGTTAAGTCTTGTACTGAGTGGCCGACAGATCGTCGGCCACATTATTTTTTACGTCGACGAATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCTCCCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTACACGGGCGGGACCATCGGGATGCAGCGTTCCGAGCAGGGTTATATACCGGTG  >  NC_000913/1850670‑1850940
                                                                                                                                        |                                                                                                                                      
cTGACCTGCGCCAACATGCGTTAAGTCTTGTACTGAGTGGCCGACAGATCGTCGGCCACATTATTTTTTACGTCGACGAATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCTccc                                                                                                                                      <  1:1272721/139‑1 (MQ=255)
   aCCTGCGCCAACATGCGTTAAGTCGTGTACTGAGTGGCCGACAGATCGTCGGCCACATTATTTTTTACGTCGACGAATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCTcccctg                                                                                                                                   <  2:1089608/139‑3 (MQ=255)
                            tGTACTGAGTGGCCGACAGATCGTGTGCCACATTATTTTTTACGTCGACGAATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCttt                                                                                                         <  1:927178/139‑1 (MQ=255)
                                   aGTGGCCGACAGATCGTCGGCCACATTATTTTTTACGTCGACGAATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTc                                                                                                                              >  1:1216019/1‑111 (MQ=255)
                                   aGTGGCCGACAGATCGTCGGCCACATTATTTTTTACGTCGACGAATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTc                                                                                                                              <  2:1216019/111‑1 (MQ=255)
                                     tGGCCGACAGATCGTCGGCCACATTATTTTTTACGTCGACGAATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATAtcat                                                                                                >  2:268512/1‑139 (MQ=255)
                                                   tcgGCCACATTATTTTTTACGTCGACGAATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCatatcaatatca                                                                                  <  2:455429/139‑1 (MQ=255)
                                                                       gTCGACGAATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCAc                                                                                                                            <  1:559494/77‑1 (MQ=255)
                                                                       gTCGACGAATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCAc                                                                                                                            >  2:559494/1‑77 (MQ=255)
                                                                         cgacgaATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACg                                                             >  2:645252/1‑138 (MQ=255)
                                                                         cgacgaATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACg                                                             <  1:645252/138‑1 (MQ=255)
                                                                          gacgaATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGtt                                                           <  1:268512/139‑1 (MQ=255)
                                                                                     ttCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATAtcatt                                                                                               >  1:1253985/1‑92 (MQ=255)
                                                                                     ttCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATAtcatt                                                                                               <  2:1253985/92‑1 (MQ=255)
                                                                                         cGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTACAcgggcggg                                            <  1:78809/139‑1 (MQ=255)
                                                                                          gCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCt                                                                                                                               <  2:93166/55‑1 (MQ=255)
                                                                                          gCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCt                                                                                                                               >  1:93166/1‑55 (MQ=255)
                                                                                                        tatTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGct                                                                                                             <  1:65102/59‑1 (MQ=255)
                                                                                                        tatTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGct                                                                                                             >  2:65102/1‑59 (MQ=255)
                                                                                                        tatTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTACACGGGCGGGACCATCGGGATGCAg                             >  2:582833/1‑139 (MQ=255)
                                                                                                        tatTTCCTTATCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTACACGGGCGGGACCATCGGGATGCAg                             >  1:1063480/1‑139 (MQ=255)
                                                                                                                 aTCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTACACGGGCGGGACCATCGGGATGCAGCGTTCCGAg                    <  2:1063480/139‑1 (MQ=255)
                                                                                                                 aTCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTACACGGGCGGGACCATCGGGATGCAGCGTTCCGAg                    <  1:97622/139‑1 (MQ=255)
                                                                                                                  tCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTac                                                     >  2:518994/1‑105 (MQ=255)
                                                                                                                  tCCGCATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCACGCAAAAGAAATCAATTTACGTTGCCTac                                                     <  1:518994/105‑1 (MQ=255)
                                                                                                                      cATAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTACACGGGCGGGACCATCGGGATGCAGCGTTCCGAGCa                  <  2:795902/136‑1 (MQ=255)
                                                                                                                      cATAATATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATAACATGCAAAAGAAATCAATTTACGTTGCCTACACGGGCGGGACCATCGAGATGCAGCGTTCCGAGCa                  >  1:795902/1‑136 (MQ=255)
                                                                                                                       aTAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTACACGGGCGGGACCATCGGGATGCAGCGTTCCGAGCAGGGt              >  1:617102/1‑139 (MQ=255)
                                                                                                                       aTAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTACACGGGCGGGACCATCGGGATGCAGCGTTCCGAGCAGGGt              >  2:786641/1‑139 (MQ=255)
                                                                                                                        tAGTATCAGGTGCGCT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTACACGGGCGGGACCATCGGGATGCAGCGTTCCGAGCAGGGtt             <  1:872304/139‑1 (MQ=255)
                                                                                                                                   gcgcT‑CCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTACACGGGCGGGACCATCGGGATGCAGCGTTCCGAGCAGGGTTATATACCGgtg  >  2:271410/1‑139 (MQ=255)
                                                                                                                                        |                                                                                                                                      
CTGACCTGCGCCAACATGCGTTAAGTCTTGTACTGAGTGGCCGACAGATCGTCGGCCACATTATTTTTTACGTCGACGAATCCTCTTCCCGCTGTTTCGCCCCATATTTCCTTATCCGCATAGTATCAGGTGCGCTCCCCCTGCCTCACGTATATACTTTTGCTCTTTCGATATCATTCATATCAATATCATGCAAAAGAAATCAATTTACGTTGCCTACACGGGCGGGACCATCGGGATGCAGCGTTCCGAGCAGGGTTATATACCGGTG  >  NC_000913/1850670‑1850940

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A