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
A10 F1 I1 R1 759 65.2 3386260 90.7% 3071337 101.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,950,559 (C)5→6 intergenic (‑37/‑273) aspS ← / → yecD aspartyl‑tRNA synthetase/isochorismatase family protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,950,5541.C97.8% 154.4 / ‑3.4 45intergenic (‑32/‑278)aspS/yecDaspartyl‑tRNA synthetase/isochorismatase family protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (20/24);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 4.67e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.65e-01

GAAGATCAGGCTACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑CCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTAC  >  NC_000913/1950418‑1950683
                                                                                                                                         |                                                                                                                                  
gAAGATCAGGCTACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑cc                                                                                                                                  >  2:1667384/1‑139 (MQ=255)
    aTCAGGCTACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑cccc‑cc                                                                                                                             <  1:752567/139‑2 (MQ=255)
           tACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGGCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTgcg                                                                                                                       <  2:1547836/139‑1 (MQ=255)
             ccAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑cccc‑cctg                                                                                                                           <  1:239129/132‑4 (MQ=255)
             ccAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑cccc‑cctg                                                                                                                           >  2:239129/1‑129 (MQ=255)
              cAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAg                                                                                                                    >  2:921656/1‑139 (MQ=255)
                   tCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGAc                                                                                                               >  2:1058888/1‑139 (MQ=255)
                    cACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGAcc                                                                                                              <  2:1679836/139‑1 (MQ=255)
                       gacgacgGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAg                                                                                                           >  2:901322/1‑139 (MQ=255)
                           acgGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGc                                                                                                       <  2:849770/139‑1 (MQ=255)
                           acgGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGc                                                                                                       <  1:1667384/139‑1 (MQ=255)
                                tGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGt                                                                                                  <  1:977711/139‑1 (MQ=255)
                                tGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGt                                                                                                  <  2:23865/139‑1 (MQ=255)
                                 gACCCAACCACACAGAGTCACCTACTCCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGtt                                                                                                 >  2:351393/1‑139 (MQ=255)
                                   cccAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAg                                                                                               <  1:901322/139‑1 (MQ=255)
                                   cccAACCACACAGAGTCACCTACTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAg                                                                                               <  1:351393/139‑1 (MQ=255)
                                             caGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTca                                                                                     >  1:660556/1‑139 (MQ=255)
                                             caGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTca                                                                                     <  1:1058888/139‑1 (MQ=255)
                                                            ccccACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGaaaaa                                                                      >  2:680602/1‑139 (MQ=255)
                                                             cccACGGGGGACAAACGGAGCTTTCCACAATATTCTGTACGCATGAGATATCCCTGTACTTAGCTGCCGGCGGATGCCCCC‑CTGCAGCGCAGGTGGCCAAGTCGCAGCGTAACCTGTATGTCACAACTGCATGaaacaa                                                                     <  2:287599/139‑1 (MQ=255)
                                                                aCGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                  <  1:921656/139‑1 (MQ=255)
                                                                 cGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTa                                                                                          <  1:1211705/114‑1 (MQ=255)
                                                                 cGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑CCCCTCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTa                                                                                          >  2:1211705/1‑114 (MQ=255)
                                                                           aCGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATg                                                                                                                                     <  1:956137/62‑1 (MQ=255)
                                                                           aCGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATg                                                                                                                                     >  2:956137/1‑62 (MQ=255)
                                                                                 cTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGaaa                                                 >  1:1046902/1‑139 (MQ=255)
                                                                                              tCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑cccc‑c                                                                                                                              >  2:972992/1‑48 (MQ=255)
                                                                                              tCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑cccc‑c                                                                                                                              <  1:972992/48‑1 (MQ=255)
                                                                                                tGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                  >  2:1251791/1‑107 (MQ=255)
                                                                                                tGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                  <  1:1251791/107‑1 (MQ=255)
                                                                                                  tACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAag                                >  2:1379746/1‑139 (MQ=255)
                                                                                                       aTGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                  >  2:1230672/1‑100 (MQ=255)
                                                                                                       aTGAGATATCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                  <  1:1230672/100‑1 (MQ=255)
                                                                                                       aTGAGATATCCCTTAACTTAGCTGCCGCCGGAAGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCt                           >  2:1006678/1‑139 (MQ=255)
                                                                                                               tCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGc                                           >  1:742869/1‑115 (MQ=255)
                                                                                                               tCCCTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGc                                           <  2:742869/115‑1 (MQ=255)
                                                                                                                 ccTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGc                                                                                              <  2:1365314/62‑1 (MQ=255)
                                                                                                                 ccTTAACTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGc                                                                                              >  1:1365314/1‑62 (MQ=255)
                                                                                                                     aaCTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGaa             >  1:1090025/1‑139 (MQ=255)
                                                                                                                      aCTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGt                                                                                                                  <  1:1111168/37‑1 (MQ=255)
                                                                                                                      aCTTAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGt                                                                                                                  >  2:1111168/1‑37 (MQ=255)
                                                                                                                         tAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGt                                                                                       <  1:459830/61‑1 (MQ=255)
                                                                                                                         tAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGt                                                                                       >  2:459830/1‑61 (MQ=255)
                                                                                                                         tAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGc          <  1:551623/138‑1 (MQ=255)
                                                                                                                         tAGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGc          >  2:551623/1‑138 (MQ=255)
                                                                                                                          aGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAg                                                                    >  2:454289/1‑79 (MQ=255)
                                                                                                                          aGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAg                                                                    <  1:454289/79‑1 (MQ=255)
                                                                                                                          aGCTGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCt        >  1:689736/1‑139 (MQ=255)
                                                                                                                             tGCCGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGt     <  2:689736/139‑1 (MQ=255)
                                                                                                                               ccGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                  >  2:936813/1‑76 (MQ=255)
                                                                                                                               ccGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                  <  1:936813/76‑1 (MQ=255)
                                                                                                                               ccGGCGGATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCATTa   <  2:1090025/139‑1 (MQ=255)
                                                                                                                                cggcggATGCCCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTAc  <  2:557498/139‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                  
GAAGATCAGGCTACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑CCCC‑CTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTAC  >  NC_000913/1950418‑1950683

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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