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
A1 F1 I1 R1 773 79.9 4112934 92.2% 3792125 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 723,528 (T)8→9 coding (887/2685 nt) kdpD ← fused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913723,5201.T95.3% 126.4 / ‑0.8 43coding (895/2685 nt)kdpDfused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base T (22/19);  total (23/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.41e-01

CCGAGAATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGATGCATA  >  NC_000913/723387‑723651
                                                                                                                                      |                                                                                                                                       
ccGAGAATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑‑tttt‑t                                                                                                                                 >  2:2043044/1‑139 (MQ=255)
            ttGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAg                                                                                                                     <  1:2043044/139‑1 (MQ=255)
            ttGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAg                                                                                                                     <  1:210091/139‑1 (MQ=255)
                          ttCACGGGCATAACCCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAATGCGCTGAGAATTGCCCGACG‑‑‑TTTT‑TTATTCCGGTAAGCGGCgcagggcagg                                                                                                       <  2:1259647/139‑1 (MQ=255)
                              cGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGtt                                                                                                   <  2:546453/139‑1 (MQ=255)
                              cGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGtt                                                                                                   >  1:1852596/1‑139 (MQ=255)
                              cGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGtt                                                                                                   >  1:222325/1‑139 (MQ=255)
                               gggCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGttt                                                                                                  >  2:1989650/1‑139 (MQ=255)
                                    tAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACa                                                                                             >  2:1751110/1‑139 (MQ=255)
                                           cTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGTCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGtt                                                                                                   <  2:280495/126‑1 (MQ=255)
                                           cTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAg                                                                                                                     >  2:687543/1‑108 (MQ=255)
                                           cTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAg                                                                                                                     <  1:687543/108‑1 (MQ=255)
                                           cTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGtt                                                                                                   >  1:280495/1‑126 (MQ=255)
                                            tACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACcgc                                                                                     <  2:222325/139‑1 (MQ=255)
                                                gCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCCCCGCGCCCAGTTCCGGCGCCAGACGTAAGGCGCGGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGc                                                                                 <  1:2020235/139‑1 (MQ=255)
                                                 cTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGt                                                                                                                        <  1:1780909/99‑1 (MQ=255)
                                                 cTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGt                                                                                                                        >  2:1780909/1‑99 (MQ=255)
                                                 cTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGttt                                                                                                  >  2:1450907/1‑121 (MQ=255)
                                                 cTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATCGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGttt                                                                                                  <  1:1450907/121‑1 (MQ=255)
                                                           cGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTAcc                                                                      <  2:828837/139‑1 (MQ=255)
                                                                        aGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTTCCCAGCCGTGACGcc                                                         >  1:1808358/1‑139 (MQ=255)
                                                                           gtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgc                                                      >  1:37717/1‑139 (MQ=255)
                                                                            ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgcc                                                     >  2:376732/1‑139 (MQ=255)
                                                                            ttGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGACAGACGCTACCCAGCCGTGACGCCAgcc                                                     >  2:1233692/1‑139 (MQ=255)
                                                                              gCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgccgc                                                   >  1:498339/1‑139 (MQ=255)
                                                                               ccGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgccgcg                                                  >  1:263749/1‑139 (MQ=255)
                                                                                cGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAg                                                                                                                     >  2:1542157/1‑71 (MQ=255)
                                                                                cGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAg                                                                                                                     <  1:1542157/71‑1 (MQ=255)
                                                                                    tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGACTTGCCCGACG‑‑‑TTTTATT‑TTCCGGTAAGCGGTGCAGGGCAgggg                                                                                                     >  1:1355318/1‑83 (MQ=255)
                                                                                    tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAgggg                                                                                                     <  2:1355318/83‑1 (MQ=255)
                                                                                           ccAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGa                                      >  2:1950551/1‑139 (MQ=255)
                                                                                             aGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGAcc                                    >  2:1407115/1‑139 (MQ=255)
                                                                                              gTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTAGCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCa                                   >  2:1289660/1‑139 (MQ=255)
                                                                                                      gcCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCg                           <  2:1852596/139‑1 (MQ=255)
                                                                                                       ccAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑‑tttt‑t                                                                                                                                 >  2:1327743/1‑36 (MQ=255)
                                                                                                       ccAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑‑tttt‑t                                                                                                                                 <  1:1327743/36‑1 (MQ=255)
                                                                                                         aGACGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTg                        >  1:1009553/1‑139 (MQ=255)
                                                                                                           aCGTAAGGCGCTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTCTTCGCTGcc                      <  2:1009553/139‑1 (MQ=255)
                                                                                                                     cTGAGAATTGCCCGACGTTTTTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTAt              >  2:1919012/1‑139 (MQ=255)
                                                                                                                     cTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCa                                                                                                >  2:1225808/1‑55 (MQ=255)
                                                                                                                     cTGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCa                                                                                                <  1:1225808/55‑1 (MQ=255)
                                                                                                                      tGAGAATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGc           <  2:37717/139‑1 (MQ=255)
                                                                                                                        agaATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCg         <  1:1950551/139‑1 (MQ=255)
                                                                                                                         gaATTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACTCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGa        <  1:1343612/139‑1 (MQ=255)
                                                                                                                           aTTGCCCGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGGCCAGTTTTTCGCTGCCGGTGTTATGGCCGATg      <  1:1989650/139‑1 (MQ=255)
                                                                                                                               cccGACGT‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTCTGGCCGATGCATa  >  2:1254138/1‑139 (MQ=255)
                                                                                                                                      |                                                                                                                                       
CCGAGAATAATCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑‑TTTT‑TT‑TTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGATGCATA  >  NC_000913/723387‑723651

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