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
A8 F50 I1 R1 163 55.0 1534755 98.6% 1513268 150.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,636,093 G→A pseudogene (275/528 nt) nohQ ← pseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,636,0930GA97.8% 122.4 / NA 46pseudogene (275/528 nt)nohQpseudogene, Qin prophage; Phage DNA packaging protein Nu1 family;Phage or Prophage Related; DNA packaging protein NU1 homolog from lambdoid prophage Qin
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (10/35);  minor base C (0/1);  total (10/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

GGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTTATAACGGCGG  >  NC_000913/1635946‑1636237
                                                                                                                                                   |                                                                                                                                                
ggAAACCGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCacac                                                                                                                                               <  1:465504/151‑1 (MQ=14)
ggAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCacac                                                                                                                                               >  2:743725/1‑151 (MQ=14)
 gAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACAcg                                                                                                                                              >  1:41794/1‑151 (MQ=14)
      cgccgcTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTaa                                                                                                                                         <  1:384686/151‑1 (MQ=14)
             gCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCGCCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGa                                                                                                                                    <  2:754289/149‑1 (MQ=14)
                ccGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCg                                                                                                                               <  1:292454/151‑1 (MQ=14)
                     aGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGt                                                                                                                          <  1:669943/151‑1 (MQ=14)
                            tCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAAt                                                                                                                   >  1:488133/1‑151 (MQ=14)
                              ccGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAg                                                                                                                 <  2:396732/151‑1 (MQ=14)
                                gTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTc                                                                                                               >  1:437471/1‑151 (MQ=14)
                                       aTACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCctggct                                                                                                        <  1:456715/151‑1 (MQ=14)
                                         aCTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCTCCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCctggctgg                                                                                                      <  1:356409/151‑1 (MQ=14)
                                         aCTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCctggctgg                                                                                                      >  2:354443/1‑151 (MQ=14)
                                            ggCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCCCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGgag                                                                                                    <  1:360471/150‑1 (MQ=14)
                                              cAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCctggctgg                                                                                                      >  1:63124/1‑146 (MQ=14)
                                                aTTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTg                                                                                               <  1:684258/151‑1 (MQ=14)
                                                            aTCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCt                                                                                   >  2:427288/1‑151 (MQ=14)
                                                                 cgACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGc                                                                              >  1:184972/1‑151 (MQ=18)
                                                                 cgACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGc                                                                              <  1:139310/151‑1 (MQ=18)
                                                                   aCAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAg                                                                            <  1:581821/151‑1 (MQ=18)
                                                                       cACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGttct                                                                        <  1:282263/151‑1 (MQ=18)
                                                                         cGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGttcttc                                                                      <  1:480907/151‑1 (MQ=18)
                                                                             aGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACt                                                                  <  2:292797/151‑1 (MQ=21)
                                                                                  aGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCg                                                             >  1:260420/1‑151 (MQ=25)
                                                                                        cGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAg                                                       <  1:549061/151‑1 (MQ=25)
                                                                                          gTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCt                                                     <  2:207700/151‑1 (MQ=25)
                                                                                          gTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCt                                                     <  2:295076/151‑1 (MQ=25)
                                                                                            ttCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCtt                                                    <  2:404904/150‑1 (MQ=25)
                                                                                              ccaccaCTGCAGCGGAGTCTCTTGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTTAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCtttt                                                  <  2:624639/150‑1 (MQ=255)
                                                                                                accacTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGt                                               <  2:633803/151‑1 (MQ=25)
                                                                                                 ccacTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGtt                                              <  1:516642/151‑1 (MQ=25)
                                                                                                     ttCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTtctc                                           >  2:664946/1‑150 (MQ=25)
                                                                                                            gAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTc                                     >  1:435996/1‑149 (MQ=25)
                                                                                                             aGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGc                                  <  1:224541/151‑1 (MQ=25)
                                                                                                                  ctGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTTGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATc                               <  2:2830/149‑1 (MQ=25)
                                                                                                                    ggCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATcc                              <  1:75092/148‑1 (MQ=25)
                                                                                                                    ggCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCtt                           <  2:381187/151‑1 (MQ=25)
                                                                                                                     gCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCt                            <  1:338177/149‑1 (MQ=25)
                                                                                                                     gCATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATGTCAGCATCCCttt                          <  2:35201/151‑1 (MQ=25)
                                                                                                                      cATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGTCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTc                         <  2:349525/151‑1 (MQ=25)
                                                                                                                      cATTTTTCAGCTCCTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTc                         <  2:437450/151‑1 (MQ=25)
                                                                                                                                  ccTGTGCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCt             <  2:258607/151‑1 (MQ=37)
                                                                                                                                       gCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTtata         <  2:574056/150‑1 (MQ=255)
                                                                                                                                       gCGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTtata         <  2:320448/150‑1 (MQ=255)
                                                                                                                                        cGTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTTATAAc       <  1:237513/151‑1 (MQ=255)
                                                                                                                                         gTCGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTTATAAcg      <  1:734498/151‑1 (MQ=39)
                                                                                                                                           cGGCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTTATAAcggc    <  1:710646/151‑1 (MQ=38)
                                                                                                                                             gCCTGCACACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTTATAAcggcgg  <  2:74898/151‑1 (MQ=38)
                                                                                                                                                   |                                                                                                                                                
GGAAAACGCCGCTGCACCGACAGGGGGATCCCGTCGAGAATACTGGCAATTTCACCTGCGATCCGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTTTTCAGCTCCTGTGCGTCGGCCTGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTCCCTGGCTGGAGATCTGTCTCGCTGGCCTGCCGCAGTTCTTCAACTTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTTCGGCATACCATCTTATAACGGCGG  >  NC_000913/1635946‑1636237

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A