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
A2 F1 I2 R1 764 42.0 2018750 95.5% 1927906 109.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,400,615 (T)7→8 intergenic (+19/‑57) hfq → / → hflX global sRNA chaperone, HF‑I, host factor for RNA phage Q beta replication/GTPase, stimulated by 50S subunit binding, Mn(2+) homeostasis regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,400,6081.T95.9% 142.1 / ‑4.5 50intergenic (+12/‑64)hfq/hflXglobal sRNA chaperone, HF‑I, host factor for RNA phage Q beta replication/GTPase, stimulated by 50S subunit binding, Mn(2+) homeostasis regulator
Reads supporting (aligned to +/- strand):  ref base . (1/0);  major base T (22/25);  minor base C (1/1);  total (24/26)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTG‑TTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTACGCAAGACAAA  >  NC_000913/4400471‑4400737
                                                                                                                                          |                                                                                                                                 
gttgtCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTG‑t                                                                                                                                  >  2:220307/1‑139 (MQ=255)
  tgtCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTG‑ttt                                                                                                                                >  1:272911/1‑139 (MQ=255)
      ccGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTG‑ttttttt                                                                                                                            <  1:220307/139‑1 (MQ=255)
                             caGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGTAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTg                                                                                                      <  2:537538/139‑1 (MQ=255)
                                      cGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGa                                                                                                                   >  2:913053/1‑117 (MQ=255)
                                      cGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGa                                                                                                                   <  1:913053/117‑1 (MQ=255)
                                      cGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCg                                                                                             <  1:379679/139‑1 (MQ=255)
                                        ccGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCt                                                                                           <  1:128726/139‑1 (MQ=255)
                                        ccGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCt                                                                                           <  2:272911/139‑1 (MQ=255)
                                          ggTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATc                                                                                                         <  1:1007436/123‑1 (MQ=255)
                                          ggTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATc                                                                                                         >  2:1007436/1‑123 (MQ=255)
                                            tGGCGGTACCAGCAGTTACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGCTCCTGCGTTCCCCGCTGATc                                                                                       <  2:684938/139‑1 (MQ=255)
                                                             aCTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCt                                                                                           <  2:739028/118‑1 (MQ=255)
                                                             aCTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCt                                                                                           >  1:739028/1‑118 (MQ=255)
                                                             aCTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATAc                                                                      >  2:463488/1‑139 (MQ=255)
                                                                  catcatGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACgg                                                                                                                      >  1:229920/1‑86 (MQ=255)
                                                                  catcatGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACgg                                                                                                                      <  2:229920/86‑1 (MQ=255)
                                                                       tGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGa                                                            <  2:485551/139‑1 (MQ=255)
                                                                        ggTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGAc                                                           <  1:614523/139‑1 (MQ=255)
                                                                         gTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCt                                                                                           <  1:833260/106‑1 (MQ=255)
                                                                         gTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCt                                                                                           >  2:833260/1‑106 (MQ=255)
                                                                         gTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGAcc                                                          >  2:912209/1‑139 (MQ=255)
                                                                           agcagcGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGt                                                        >  2:685352/1‑139 (MQ=255)
                                                                           agcagcGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATATATTTAGAGGGTTATACGCTTGTTTGACCGt                                                        >  1:80151/1‑139 (MQ=255)
                                                                           agcagcGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTG‑TTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGtt                                                       >  2:777846/1‑139 (MQ=255)
                                                                            gcagcGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTaga                                                                               >  1:523897/1‑115 (MQ=255)
                                                                            gcagcGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTaga                                                                               <  2:523897/115‑1 (MQ=255)
                                                                                cgcgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCt                                                                                                       >  2:651266/1‑87 (MQ=255)
                                                                                cgcgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCt                                                                                                       <  1:651266/87‑1 (MQ=255)
                                                                                cgcgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTa                                                      <  2:683108/136‑1 (MQ=255)
                                                                                cgcgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTa                                                      >  1:683108/1‑136 (MQ=255)
                                                                                 gcgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTatgat                                                  >  1:856767/1‑139 (MQ=255)
                                                                                  cgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGa                                                                                                                   <  2:964926/73‑1 (MQ=255)
                                                                                  cgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGa                                                                                                                   >  1:964926/1‑73 (MQ=255)
                                                                                  cgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCg                                                                                             >  1:518749/1‑95 (MQ=255)
                                                                                  cgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCg                                                                                             <  2:518749/95‑1 (MQ=255)
                                                                                  cgcAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTatgatg                                                 >  1:153011/1‑139 (MQ=255)
                                                                                      gAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTgg                                             >  1:820284/1‑139 (MQ=255)
                                                                                          aCTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAg                                         <  2:153011/139‑1 (MQ=255)
                                                                                            ttCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCa                                       <  1:685352/139‑1 (MQ=255)
                                                                                               cgcgCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGc                                    <  1:912209/139‑1 (MQ=255)
                                                                                                 cgcAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCgg                                  >  2:271930/1‑139 (MQ=255)
                                                                                                   cAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTa                                <  2:820284/139‑1 (MQ=255)
                                                                                                   cAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTa                                >  1:945113/1‑139 (MQ=255)
                                                                                                      cAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATAc                                                                      <  2:999838/98‑1 (MQ=255)
                                                                                                      cAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATAc                                                                      >  1:999838/1‑98 (MQ=255)
                                                                                                         gACAGCGAAGAAGCCGCATACGGTTTCCGGCTGCTCTTTTTACACGGGTAGCCAGCGATCCTGCGTTGCCCGCTGCTCTATCCAGAGGGCTATACGCTAGTTTGACCGTTATGATGCTGGTCACCAGGCGCCACTggca                          >  1:246881/1‑137 (MQ=255)
                                                                                                              cGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCt                                                                                           >  2:35362/1‑69 (MQ=255)
                                                                                                              cGAAGAAACCGAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCt                                                                                           <  1:35362/69‑1 (MQ=255)
                                                                                                              cGAAGAAACCGAATAAGGTTTCGGGCTGCTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACAt                     <  2:878272/139‑1 (MQ=255)
                                                                                                                        gAATAAGGTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTACg           <  1:463488/139‑1 (MQ=255)
                                                                                                                               gTTTCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTACGCAAGACa    >  1:289516/1‑139 (MQ=255)
                                                                                                                                 ttCGGGCTGTTTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTACGCAAGACaaa  <  2:289516/139‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                 
GTTGTCCCGTCTCGCCCGGTTTCTCATCACAGTAACAACGCCGGTGGCGGTACCAGCAGTAACTACCATCATGGTAGCAGCGCGCAGAATACTTCCGCGCAACAGGACAGCGAAGAAACCGAATAAGGTTTCGGGCTG‑TTTTTTTACACGGGGAGCCAGCGATCCTGCGTTCCCCGCTGATCTATTTAGAGGGTTATACGCTTGTTTGACCGTTATGATGCTGGTGAGCAGGCGGTACTGGTACACATCTATTTTACGCAAGACAAA  >  NC_000913/4400471‑4400737

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A