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
A4 F50 I2 R1 104 44.1 1376607 98.9% 1361464 150.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,664,363 (G)6→7 coding (256/729 nt) gadW ← transcriptional activator of gadA and gadBC; repressor of gadX

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,664,3571.G94.6% 131.6 / ‑1.2 38coding (262/729 nt)gadWtranscriptional activator of gadA and gadBC; repressor of gadX
Reads supporting (aligned to +/- strand):  ref base . (0/2);  new base G (19/16);  total (19/19)
Fisher's exact test for biased strand distribution p-value = 2.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AACAGTGCTGATGCTATTGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑GGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCG  >  NC_000913/3664208‑3664502
                                                                                                                                                      |                                                                                                                                                  
aaCAGTGCTGATGCTATTGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑g                                                                                                                                                   <  1:129226/151‑1 (MQ=255)
             cTATTGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTgg                                                                                                                                      >  2:297733/1‑151 (MQ=255)
                     aaGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGttaattaa                                                                                                                              <  2:550538/151‑1 (MQ=255)
                                tCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCtt                                                                                                                   >  2:52967/1‑151 (MQ=255)
                                  aGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTg                                                                                                                 <  1:234855/151‑1 (MQ=255)
                                  aGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTg                                                                                                                 >  1:63461/1‑151 (MQ=255)
                                      ctttcttATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCtgt                                                                                                             >  2:234529/1‑151 (MQ=255)
                                       tttcttATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCtgtg                                                                                                            >  2:237049/1‑151 (MQ=255)
                                        ttcttATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCtgt                                                                                                             <  2:649434/149‑1 (MQ=255)
                                        ttcttATAATAAAACATCGTAAAAAAGGAAAGTTGAAGAAAATGGTTCAGTTAGGGTTATTTTACCCTGACTTATTTAAATTTATCAAAAATACCATTCCCTACGGGCTG‑GGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTgtgt                                                                                                           <  2:307115/150‑1 (MQ=255)
                                         tcttATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTgtgt                                                                                                           >  2:201738/1‑150 (MQ=255)
                                           ttATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAAc                                                                                                        >  2:298503/1‑151 (MQ=255)
                                            tATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATCTTGCTCATTATCGGTGAATTTAGCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATAGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTaa                                                                                                         <  1:339455/149‑1 (MQ=255)
                                                 gaAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTaa                                                                                                   >  1:159907/1‑150 (MQ=255)
                                                  aaaaCATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTCTCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTaaa                                                                                                  >  2:110476/1‑150 (MQ=255)
                                                             aaaCAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑GGGCGGGTGGCTTGTTAATTAACAAACGGTCTTTGCTGTCTAACCCTAAATTGCGTGGTAg                                                                                       <  1:684867/150‑1 (MQ=255)
                                                                  ggAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACg                                                                                 <  1:285486/151‑1 (MQ=255)
                                                                     aaGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAat                                                                              <  1:276827/151‑1 (MQ=255)
                                                                     aaGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAat                                                                              <  2:138341/151‑1 (MQ=255)
                                                                        gTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATAtt                                                                           <  2:571160/151‑1 (MQ=255)
                                                                         tAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATAttt                                                                          >  1:36741/1‑151 (MQ=255)
                                                                         tAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATAttt                                                                          >  1:653022/1‑151 (MQ=255)
                                                                          agagCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATAtttt                                                                         >  1:313094/1‑151 (MQ=255)
                                                                           gagCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTg                                                                        >  2:503824/1‑151 (MQ=255)
                                                                                                            ggATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATc                                       <  1:132848/151‑1 (MQ=255)
                                                                                                                tCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAg                                    <  1:294749/150‑1 (MQ=255)
                                                                                                                 cATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAgtc                                  >  1:502222/1‑151 (MQ=255)
                                                                                                                           aTCAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATc                        >  2:84781/1‑151 (MQ=255)
                                                                                                                             cAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCg                      <  1:393709/151‑1 (MQ=255)
                                                                                                                             cAAAAATCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTGTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCg                      <  1:439337/151‑1 (MQ=255)
                                                                                                                              aaaaaTCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCgg                     >  1:145461/1‑151 (MQ=255)
                                                                                                                                 aaTCGCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTg                   >  2:29017/1‑150 (MQ=255)
                                                                                                                                     gCCGTCACCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACa               >  1:137470/1‑150 (MQ=255)
                                                                                                                                           aCCAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCa        <  2:440606/151‑1 (MQ=255)
                                                                                                                                             cAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCaaa      <  1:579819/151‑1 (MQ=255)
                                                                                                                                             cAGCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCaa       >  1:560863/1‑150 (MQ=255)
                                                                                                                                               gCGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAAt    <  1:675038/151‑1 (MQ=255)
                                                                                                                                                cGGCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATc   <  1:52967/151‑1 (MQ=255)
                                                                                                                                                 ggCATGGGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCg  <  2:495409/151‑1 (MQ=255)
                                                                                                                                                      |                                                                                                                                                  
AACAGTGCTGATGCTATTGAAAAGTAAGGGGATCAGTTCTTTCTTATGAGAAAACATCGATAAACAGGAAAGGTAGAGCATATTGCTCAGTATCGGTGAATTTACCCCGGATTCATTGAAGCTATCAAAAATCGCCGTCACCAGCGGCAT‑GGG‑GGGTGACTGGTTAATTAACAAACGGTCTTTGCTGTGTAACCCTAAATTGCGTGGTAGCTGACGAATATTTTGTAAGTAATGGCAAACTGTCAGCTCATCGATATCCAGTCGTCGCGTATCCGGTGAACAAAACGCAAAATCG  >  NC_000913/3664208‑3664502

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A