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
A7 F1 I1 R1 776 60.0 3074904 90.1% 2770488 104.4

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.C98.3% 200.0 / ‑3.5 58intergenic (‑32/‑278)aspS/yecDaspartyl‑tRNA synthetase/isochorismatase family protein
Reads supporting (aligned to +/- strand):  ref base . (1/0);  new base C (27/30);  total (28/30)
Fisher's exact test for biased strand distribution p-value = 4.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.29e-01

ATGAAGATCAGGCTACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑C‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTA  >  NC_000913/1950416‑1950682
                                                                                                                                           |                                                                                                                                 
aTGAAGATCAGGCTACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATg                                                                                                                                    >  1:417363/1‑139 (MQ=255)
           gCTACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACATAGCTGCCGGCGGATGCC‑CCCctgctg                                                                                                                        <  2:991526/139‑1 (MQ=255)
               ccAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCa                                                                                                                    >  1:172451/1‑139 (MQ=255)
                     tCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGAc                                                                                                              >  1:1464023/1‑139 (MQ=255)
                           cgacgGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTc                                                                                                        <  1:908347/139‑1 (MQ=255)
                                gTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGc                                                                                                   <  2:1457332/139‑1 (MQ=255)
                                         aCCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATAACCCTTAACTTAGCTGCCGGCGGATG‑CACCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGt                                                                                          >  2:289184/1‑139 (MQ=255)
                                                     cACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑c‑ccccc                                                                                                                            <  1:523000/92‑2 (MQ=255)
                                                     cACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑c‑ccccc                                                                                                                            >  2:523000/1‑91 (MQ=255)
                                                      aCCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACtga                                                                             <  2:1464023/139‑1 (MQ=255)
                                                            tgcCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCa                                                                                                                    <  1:614448/94‑1 (MQ=255)
                                                            tgcCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCa                                                                                                                    >  2:614448/1‑94 (MQ=255)
                                                              ccccACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAAc                                                                                >  2:775597/1‑128 (MQ=255)
                                                              ccccACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAAc                                                                                <  1:775597/128‑1 (MQ=255)
                                                              ccccACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGaaaaa                                                                     >  1:1035512/1‑139 (MQ=255)
                                                                  aCGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCACAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                 <  2:172451/139‑1 (MQ=255)
                                                                   cGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCg                                                                                                       <  2:676156/100‑1 (MQ=255)
                                                                   cGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCg                                                                                                       >  1:676156/1‑100 (MQ=255)
                                                                        gACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCtat                                                           >  1:37514/1‑139 (MQ=255)
                                                                                 aGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                 >  2:736884/1‑124 (MQ=255)
                                                                                 aGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                 <  1:736884/124‑1 (MQ=255)
                                                                                  gCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCg                                                                                                       >  2:1042997/1‑85 (MQ=255)
                                                                                  gCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCg                                                                                                       <  1:1042997/85‑1 (MQ=255)
                                                                                  gCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                 >  2:819779/1‑123 (MQ=255)
                                                                                  gCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                 <  1:819779/123‑1 (MQ=255)
                                                                                  gCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGaa                                                 >  1:73379/1‑139 (MQ=255)
                                                                                   ctatCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATCTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGaaa                                                <  1:41258/136‑1 (MQ=255)
                                                                                      tCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTc                                             >  2:1522098/1‑139 (MQ=255)
                                                                                      tCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTc                                             >  2:1419057/1‑139 (MQ=255)
                                                                                       ccACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                 >  1:461551/1‑118 (MQ=255)
                                                                                       ccACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAggc                                                                 <  2:461551/118‑1 (MQ=255)
                                                                                             tatTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGAcc                                                                                                             <  1:1093324/68‑1 (MQ=255)
                                                                                             tatTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGAcc                                                                                                             >  2:1093324/1‑68 (MQ=255)
                                                                                                tCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCg                                   >  2:26603/1‑139 (MQ=255)
                                                                                                  tttACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCGGTATGTCACAACTGAATGAAAAAAGGCGGCCATTATACTGGAAATTCTGCCGCACCGTa                                 <  2:73379/137‑1 (MQ=255)
                                                                                                  tGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACt                                                     <  2:1305369/119‑1 (MQ=255)
                                                                                                  tGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACt                                                     >  1:1305369/1‑119 (MQ=255)
                                                                                                       gCATGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGc                            >  2:1181229/1‑139 (MQ=255)
                                                                                                         aTGAGATATCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCt                          >  2:791411/1‑139 (MQ=255)
                                                                                                               tatCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGGATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCcg                    <  1:289184/139‑1 (MQ=255)
                                                                                                                 tCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGAcc                                                                                                             <  1:1525213/48‑1 (MQ=38)
                                                                                                                 tCCCTTAACTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGAcc                                                                                                             >  2:1525213/1‑48 (MQ=38)
                                                                                                                       aaCTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGaa            <  1:791411/139‑1 (MQ=255)
                                                                                                                        aCTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAAc           >  2:406797/1‑139 (MQ=255)
                                                                                                                         cTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAag                               >  1:799381/1‑118 (MQ=255)
                                                                                                                         cTTAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAag                               <  2:799381/118‑1 (MQ=255)
                                                                                                                          ttAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGc         <  2:1035512/139‑1 (MQ=255)
                                                                                                                           tAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTg                                                                                           >  2:450291/1‑56 (MQ=39)
                                                                                                                           tAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTg                                                                                           <  1:450291/56‑1 (MQ=39)
                                                                                                                           tAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTa                                 >  1:425281/1‑114 (MQ=255)
                                                                                                                           tAGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTa                                 <  2:425281/114‑1 (MQ=255)
                                                                                                                            aGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGc                                                                                                   <  1:810221/47‑1 (MQ=38)
                                                                                                                            aGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGc                                                                                                   >  2:810221/1‑47 (MQ=38)
                                                                                                                            aGCTGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCt       <  2:37514/139‑1 (MQ=255)
                                                                                                                               tGCCGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGt    <  1:1522098/139‑1 (MQ=255)
                                                                                                                                 ccGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCta                                                            >  2:227841/1‑81 (MQ=255)
                                                                                                                                 ccGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCta                                                            <  1:227841/81‑1 (MQ=255)
                                                                                                                                 ccGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTa  <  1:406797/139‑1 (MQ=255)
                                                                                                                                 ccGGCGGATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTa  <  1:26603/139‑1 (MQ=255)
                                                                                                                                   ggcggATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAACAg                                                                   >  2:1509263/1‑72 (MQ=255)
                                                                                                                                   ggcggATGCC‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAg                                                                   <  1:1509263/72‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                 
ATGAAGATCAGGCTACCAAGATCACGACGACGGTTGACCCAACCACACAGAGTCACCTGCTGCCCCACGTGGGACAAACGGAGCTGTCCACAATATTCTGTACGCATGAGATATCCCTTAACTTAGCTGCCGGCGGATG‑C‑CCCCTGCTGCGCAGGTGACCAAGTCGCAGCGTTAGCTGTATGTCACAACTGAATGAAAAAAGGCGGCTATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGGCCCGCGCTGGAACGCCTCGTTA  >  NC_000913/1950416‑1950682

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