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 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.T94.4% 161.5 / 2.2 54coding (895/2685 nt)kdpDfused sensory histidine kinase in two‑component regulatory system with KdpE: signal sensing protein
Reads supporting (aligned to +/- strand):  ref base . (0/3);  new base T (27/24);  total (27/27)
Fisher's exact test for biased strand distribution p-value = 2.36e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

TCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGA  >  NC_000913/723397‑723645
                                                                                                                            |                                                                                                                               
tCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTa                                                                                                                 >  2:471418/1‑139 (MQ=255)
tCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTa                                                                                                                 >  1:1436189/1‑139 (MQ=255)
  ttGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAg                                                                                                               <  1:471418/139‑1 (MQ=255)
   tGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGc                                                                                                              >  2:1454555/1‑139 (MQ=255)
       gagaTTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTg                                                                                                          <  2:1211180/139‑1 (MQ=255)
               gTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTgcagggcag                                                                                                  <  2:1436189/139‑1 (MQ=255)
               gTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTgcagggcag                                                                                                  >  1:789909/1‑139 (MQ=255)
                        cATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTgcagggcagg                                                                                                 <  1:1449916/131‑1 (MQ=255)
                        cATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTgcagggcagg                                                                                                 >  2:1449916/1‑131 (MQ=255)
                        cATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCaa                                                                                         >  1:1025189/1‑139 (MQ=255)
                                       cTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTACGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCACCATACACCGCGTGcc                                                                          <  2:1025189/139‑1 (MQ=255)
                                          tctcTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTg                                                                                                          >  1:1134795/1‑104 (MQ=255)
                                          tctcTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTg                                                                                                          <  2:1134795/104‑1 (MQ=255)
                                            tctTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACg                                                                     <  1:459034/139‑1 (MQ=255)
                                              ttCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCt                                                                   >  2:680829/1‑139 (MQ=255)
                                                 cGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTAcc                                                                >  1:919038/1‑139 (MQ=255)
                                                   cTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAA‑TGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTgcagggcag                                                                                                  >  1:1113478/1‑102 (MQ=255)
                                                   cTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAA‑TGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTgcagggcag                                                                                                  <  2:1113478/102‑1 (MQ=255)
                                                      gATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGGCGTAAGGCGCTGAGAATTGCCCGACGTTTT‑TTTTTTCCGGTAAGCGGTg                                                                                                          <  1:362635/93‑1 (MQ=255)
                                                      gATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGTTTT‑TTTTTTCCGGTAAGCGGTg                                                                                                          >  2:362635/1‑93 (MQ=255)
                                                      gATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGcc                                                           <  1:680829/139‑1 (MQ=255)
                                                                tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAg                                                                                                               <  2:530919/77‑1 (MQ=255)
                                                                tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAg                                                                                                               >  1:530919/1‑77 (MQ=255)
                                                                tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGtt                                                                                             <  1:751863/95‑1 (MQ=255)
                                                                tgtTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGtt                                                                                             >  2:751863/1‑95 (MQ=255)
                                                                      cGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGcc                                                           >  1:1476349/1‑123 (MQ=255)
                                                                      cGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGcc                                                           <  2:1476349/123‑1 (MQ=255)
                                                                          tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgccg                                              <  2:1118084/132‑1 (MQ=255)
                                                                          tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAgccg                                              >  1:1118084/1‑132 (MQ=255)
                                                                          tcCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCt                                       >  2:818747/1‑139 (MQ=255)
                                                                            cgcgCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTgcg                                    <  2:1153560/139‑1 (MQ=255)
                                                                             gcgcCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAAGTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTgcg                                    <  1:979595/139‑1 (MQ=255)
                                                                                  cAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAg                                                                                                               >  2:931312/1‑59 (MQ=39)
                                                                                  cAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑TTCTTTTTTCCGGTAAg                                                                                                               <  1:931312/59‑1 (MQ=39)
                                                                                             ccAGACGTAAGGCGCTGAGAATTGCCCGACGTTTT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCg                     >  2:1235107/1‑139 (MQ=255)
                                                                                             ccAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTg                                                                                                          >  1:204894/1‑53 (MQ=255)
                                                                                             ccAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTg                                                                                                          <  2:1189470/53‑1 (MQ=255)
                                                                                             ccAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTg                                                                                                          >  1:1189470/1‑53 (MQ=255)
                                                                                             ccAGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTg                                                                                                          <  2:204894/53‑1 (MQ=255)
                                                                                               aGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAg                                                                                                               >  2:558179/1‑46 (MQ=39)
                                                                                               aGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAg                                                                                                               <  1:558179/46‑1 (MQ=39)
                                                                                               aGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGTGTGcc                                                                          >  1:946724/1‑83 (MQ=255)
                                                                                               aGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTg                  >  1:276656/1‑139 (MQ=255)
                                                                                               aGACGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTg                  >  2:1379500/1‑139 (MQ=255)
                                                                                               aGACGTAAGGCGCTGAGAATTGCCCGACG‑‑tt‑ttttt                                                                                                                        >  1:1260018/1‑36 (MQ=255)
                                                                                               aGACGTAAGGCGCTGAGAATTGCCCGACG‑‑tt‑ttttt                                                                                                                        <  2:1260018/36‑1 (MQ=255)
                                                                                               aGACGTAAGGCGCTGAGAATTGCCCGACG‑‑TTCTTTTTTCCGTTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGcc                                                                          <  2:946724/83‑1 (MQ=255)
                                                                                                 aCGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAg                                                                                                               <  1:580927/44‑1 (MQ=38)
                                                                                                 aCGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAg                                                                                                               >  2:580927/1‑44 (MQ=38)
                                                                                                 aCGTAAGGCGCTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGcc                <  2:1463941/139‑1 (MQ=255)
                                                                                                           cTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCg               <  1:760773/130‑1 (MQ=255)
                                                                                                           cTGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCg               >  2:760773/1‑130 (MQ=255)
                                                                                                            tGAGAATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGc     >  1:1519348/1‑139 (MQ=255)
                                                                                                               gaATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGa  <  2:1519348/139‑1 (MQ=255)
                                                                                                               gaATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGa  <  1:1454555/139‑1 (MQ=255)
                                                                                                               gaATTGCCCGACGT‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGa  <  2:919038/139‑1 (MQ=255)
                                                                                                                            |                                                                                                                               
TCTTGCCGAGATTATGTTCACGGGCATAACGCACTACCGCTTTCTCTTCCGCTGGATCAGAAAGTGTTGCCGTCTCCGCGCCCAGTTCCTGCGCCAGACGTAAGGCGCTGAGAATTGCCCGACG‑‑TT‑TTTTTTCCGGTAAGCGGTGCAGGGCAGGGGTTTCAACATACACCGCGTGCCAGACGCTACCCAGCCGTGACGCCAGCCGCGCCGCTGCGCGGACCAGTTTTTCGCTGCCGGTGTTATGGCCGA  >  NC_000913/723397‑723645

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A